Ab Initio State Research Articles

Direct or Indirect ESPT Mechanism in CFP psamFP488? A Theoretical-Computational Investigation

Fluorescent Proteins are widely studied for their multiple applications in technological and biotechnological fields. Despite this, they continue to represent a challenge in terms of a complete understanding of all the non-equilibrium photo-induced processes that rule their properties. In this context, a theoretical-computational approach can support experimental results in unveiling and understanding the processes taking place after electronic excitation. A non-standard cyan fluorescent protein, psamFP488, is characterized by an absorption maximum that is blue-shifted in comparison to other cyan fluorescent proteins. This protein is characterized by an extended Stokes shift and an ultrafast (170 fs) excited state proton transfer. In this work, a theoretical-computational study, including excited state ab initio dynamics, is performed to help understanding the reaction mechanism and propose new hypotheses on the role of the residues surrounding the chromophore. Our results suggest that the proton transfer could be indirect toward the acceptor (Glu167) and involves other residues surrounding the chromophore, despite the ultrafast kinetics.

Time-Resolved Vibrational Analysis of Excited State Ab Initio Molecular Dynamics to Understand Photorelaxation: The Case of the Pyranine Photoacid in Aqueous Solution.

We present a novel time-resolved vibrational analysis for studying photoinduced nuclear relaxation. Generalized modes velocities are defined from ab initio molecular dynamics and wavelet transformed, providing the time localization of vibrational signals in the electronic excited state. The photoexcited pyranine in aqueous solution is presented as a case study. The transient and sequential activation of the simulated vibrational signals is in good agreement with vibrational dynamics obtained from femtosecond stimulated Raman spectroscopy data.

‘Beat Your Plowshares into Swords and Your Pruninghooks into Spears’: A Contextual Critique of Expulsion Decisions and Appeal Rights in the United Kingdom

The putative question is whether the United Kingdom complies with its treaty obligations under International Human Rights Law (IHRL) in the expulsion of migrants? The debate is that expulsion laws as they stand may have been contrived to enhance deportability or removability. It is further argued that the ever increasing and shifting pattern of deportation laws (some of which are retroactive) appears to violate the basic principles of human rights norms. This is heightened by the fact that these laws are either discretionary or couched in rigid terms leaving less chance for compassionate considerations even in the light of unclear judicial interpretation given to some of these expulsion laws. Although, States are afforded some discretion as to the manner in which they conform to their obligations under IHRL, that discretion, however, must not result in the practical denial of the minimum procedural safeguards needed to protect the migrant against arbitrary expulsion. By certifying decisions regarding expulsion, the paper finds that the State ab initio creates the amphitheater for expulsion of migrants. The argument is that the dichotomy between an ‘immigration decision’ and ‘non-immigration decision’ is a false one as it is probably anchored with the apparent intention of achieving expulsion of migrants from the UK in an ostensibly hostile environment. It is curious that the irregular migrant who makes an application (usually by payment of a fee) to the Home Office to regularize his stay which was eventually refused will not be accorded a right of appeal simply because, the State sees such applications as not befitting of a right of appeal. It is therefore difficult to justify the rationale to deny a right of appeal to a migrant or to dichotomize between an immigration decision and a non-immigration decision in the light of the immigration rules. The doctrinal methodology is applied in this paper.

A concise nodal-based derivation of the floating frame of reference formulation for displacement-based solid finite elements

The Floating Frame of Reference Formulation (FFRF) is one of the most widely used methods to analyze flexible multibody systems subjected to large rigid-body motion but small strains and deformations. The FFRF is conventionally derived via a continuum mechanics approach. This tedious and circuitous approach, which still attracts attention among researchers, yields so-called inertia shape integrals. These unhandy volume integrals, arising in the FFRF mass matrix and quadratic velocity vector, depend not only on the degrees of freedom, but also on the finite element shape functions. That is why conventional computer implementations of the FFRF are laborious and error prone; they require access to the algorithmic level of the underlying finite element code or are restricted to a lumped mass approximation. This contribution presents a nodal-based treatment of the FFRF to bypass these integrals. Each flexible body is considered in its spatially discretized state ab initio, wherefore the integrals are replaced by multiplications by a constant finite element mass matrix. Besides that, this approach leads to a simpler and concise but rigorous derivation of the equations of motion. The steps to obtain the inertia-integral-free equations of motion (in 2D and 3D spaces) are presented in a clear and comprehensive way; the final result provides ready-to-implement equations of motion without a lumped mass approximation, in contrast to the conventional formulation.

Unveiling anharmonic coupling by means of excited state ab initio dynamics: application to diarylethene photoreactivity.

In this work, excited state ab initio molecular dynamics together with a time resolved vibrational analysis is employed to shed light on the vibrational photoinduced dynamics of a well-known diarylethene molecule experiencing a ring opening reaction upon electronic excitation. The photoreactivity of diarylethenes is recognized to be controlled by a non-adiabatic intersection point between the ground and the first excited state surfaces. The computation of an energy scan, along a suitable reaction coordinate, allows us to identify the region of potential energy surfaces in which the ground (S0) and the first excited (S1) state are well separated. The adiabatic sampling of that region in S1 shows that in the first 3 picoseconds, the central CC bond, which is subject to break, oscillates in an antiphase with respect to the energy gap ΔE(S1 - S0). A multiresolution analysis based on the wavelet transform was then applied to the structural parameters extracted from the excited state dynamics. The wavelet maps show characteristic oscillations of the frequencies, mainly CC stretching and CCC bending localized on the central 4-ring moiety. Moreover, we have identified the main frequency (methyl wagging motion) involved in the modulation of these oscillations. The anharmonic coupling within a group of vibrational modes was therefore highlighted, in good agreement with experimental evidence. For the first time, a quantitative analysis of time resolved signals from a wavelet transform/ab initio molecular dynamics approach was performed.

Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations.

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H)-ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale of this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.

Spectral method for efficient computation of time-dependent phenomena in complex lasers

Studying time-dependent behavior in lasers is analytically difficult due to the saturating non-linearity inherent in the Maxwell-Bloch equations and numerically demanding because of the computational resources needed to discretize both time and space in conventional FDTD approaches. We describe here an efficient spectral method to overcome these shortcomings in complex lasers of arbitrary shape, gain medium distribution, and pumping profile. We apply this approach to a quasi-degenerate two-mode laser in different dynamical regimes and compare the results in the long-time limit to the Steady State Ab Initio Laser Theory (SALT), which is also built on a spectral method but makes a more specific ansatz about the long-time dynamical evolution of the semiclassical laser equations. Analyzing a parameter regime outside the known domain of validity of the stationary inversion approximation, we find that for only a narrow regime of pump powers the inversion is not stationary, and that this, as pump power is further increased, triggers a synchronization transition upon which the inversion becomes stationary again. We provide a detailed analysis of mode synchronization (aka cooperative frequency locking), revealing interesting dynamical features of such a laser system in the vicinity of the synchronization threshold.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Structural parameters of the ground states of the quasi‐stable diatomic anions CO−, BF−, and BCl− as obtained by conventional Ab Initio methods

The experimental electron affinity (EA) of CO(X1Σ+) is −1.5 eV, signifying the metastability of the CO−(X2Π) anion. The electronic structure and bonding of CO−, BF−, and BCl− vis‐à‐vis their neutral counterparts have been studied by conventional coupled‐cluster (CCSD(T)) and multireference (MRCI) methods. Our results are in agreement with experiment for the CO/CO− system, indicating as well the metastable nature of the BF−(X2Π) and BCl−(X2Π) anions, their MRCI EAs being −0.8 ± 0.1 and −0.3 ± 0.1 eV, respectively. Our work clearly shows the usefulness of stationary state ab initio methods to the elucidation of metastable species. © 2015 Wiley Periodicals, Inc.

Structure of a uranyl peroxo complex in aqueous solution from first-principles molecular dynamics simulations

Static ab initio and density-functional computations, as well as Car-Parrinello molecular dynamics simulations in aqueous solution are reported for [UO2(OH)(κ(2)-O2)(H2O)2](-) and [UO2(OH)2(κ(1)-O2H)(H2O)](-). Whereas the κ(1)-hydroperoxo isomer is found to be more stable than the κ(2)-peroxo form in the gas phase, the order of stability is reversed in explicit bulk solution. Based on free energies from thermodynamic integration (BLYP functional), the peroxo form is favoured by ca. 32 kJ mol(-1) in water. This stabilisation is discussed in terms of the hydration shells about the individual ligands and dipole moments of the complexes in water, and highlights the importance of explicit solute-solvent interactions and bulk solvation for the speciation of uranyl(vi) compounds.

Ab initio static and molecular dynamics studies of helium behavior in beryllium

Beryllium is an effective neutron multiplier material widely exploited in nuclear applications. It will be used in the helium-cooled beryllium pebble bed of fusion reactor blankets for increasing the efficiency of tritium production. Macroscopic effects of irradiation (e.g., swelling) on beryllium are greatly influenced by accumulated transmutation helium. Atomic scale simulations of beryllium behavior under irradiation are necessary for understanding the basic mechanisms and reliable prediction of microstructural changes.In this study, we investigate the behavior of interstitial and substitutional helium, its diffusion pathways and interaction with point defects present in irradiated beryllium by means of static and molecular dynamics ab initio simulations. It was shown that a mixed dumbbell consisting of self-interstitial and helium atoms represents the ground-state configuration for interstitial helium. At low temperatures, the mixed dumbbell migrates in the basal plane through a series of in-basal-plane rotations, while at higher temperatures it jumps also between adjacent basal planes.It was revealed that, as in many other metals, interstitial helium atoms are bound to each other (Eb∼1eV). In beryllium, two mixed dumbbells meet each other so that helium atoms are the nearest neighbors, whereas the helium pair can be oriented either in- or out-of-basal plane. Diffusion modes of the pair are discussed.In addition, it was found that helium is very strongly bound to vacancies: the binding energy of more than 3eV found by static ab initio calculations suggests that helium is unlikely to be released from a mono-vacancy at temperatures below the melting point. As has been shown previously, vacancy clusters are unstable in beryllium. This study shows that the addition of helium stabilizes di-vacancies. Thus, it is confirmed that the presence of transmutation gas is necessary for the development of a porous microstructure in beryllium.

Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines.

First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds. The conformational analysis of the studied compounds has been carried out at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory. The influence of steric and electronic effects on the cyclic hydrogen bonding has been analysed. The extent of the proton delocalization has been modified by the substituents according to the sequence: hydrogen < phenyl < methyl. This fact is verified by the spectroscopic and structural data as well as the energy potential curve. A prevalence of the keto-enamine tautomeric form has been observed in the static ab initio and DFT models, and confirmed by the first-principles MD.Electronic supplementary materialThe online version of this article (doi:10.1007/s10822-012-9597-3) contains supplementary material, which is available to authorized users.

Interaction of Na, Mg, Al, Si with carbon nanotube (CNT): NMR and IR study

A Quantum Mechanics (QM) is used for investigated the nature of metals transport and interaction with single-walled carbon nanotubes (SWCNTs) inter membranes. Metal species can be transported actively by a combination of SWCNT-membranes conducting channels that have been used for bio-molecular and detection. This study is based on the interaction of Na, Mg, Al, and Si with the structural features of SWCNTs in the ground state ab initio, HF theory and DFT calculation have been performed with the program Gaussian A7 package suite of programs. We used HF and DFT (B3LYP) method for calculation energy, chemical shift nucleus magnetic resonance and proportion thermodynamic by DFT-IR and DFT-NMR for RWCNT in absence and presence metals. The basis set used 6-31G and 6-31G* that increasing electronegativity metals increased the total energy. The proportion SWCNTs were changed by them. In this study presented a comprehensive on effects of metals on SWCNTs, which are on theirs electronic structure, and transfer of charge from metal to SWCNTs. The results are presented for T = 310 K, the temperature of human’s body.

Multi-level Modeling of Silica–Template Interactions During Initial Stages of Zeolite Synthesis

Zeolite synthesis is driven by structure-directing agents, such as tetrapropyl ammonium ions (TPA+) for Silicalite-1 and ZSM-5. However, the guiding role of these organic templates in the complex assembly to highly ordered frameworks remains unclear, limiting the prospects for advanced material synthesis. In this work, both static ab initio and dynamic classical modeling techniques are employed to provide insight into the interactions between TPA+ and Silicalite-1 precursors. We find that as soon as the typical straight 10-ring channel of Silicalite-1 or ZSM-5 is formed from smaller oligomers, the TPA+ template is partially squeezed out of the resulting cavity. Partial retention of the template in the cavity is, however, indispensable to prevent collapse of the channel and subsequent hydrolysis.

Structure and Stability of VO2+ in Aqueous Solution: A Car—Parrinello and Static ab initio Study.

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Intramolecular SN2 Reaction Caused by Photoionization of Benzene Chloride−NH3 Complex: Direct ab Initio Molecular Dynamics Study

Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.

Elastic quantum transport calculations using auxiliary periodic boundary conditions

An efficient new method is presented to calculate the quantum transports using periodic boundary conditions. This method allows the use of conventional ground state ab initio programs without big changes. The computational effort is only a few times of a normal ground state calculation, thus it makes accurate quantum transport calculations for large systems possible.

Ionization Dynamics of the Small-Sized Water Clusters: A Direct Ab Initio Trajectory Study

The ionization dynamics of the water clusters (H 2 O) n (n = 3-6) have been investigated by means of the full-dimensional direct ab initio trajectory method. The static ab initio and DFT calculations were carried out at the HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels, whereas the direct ab initio trajectory calculations were performed at the HF/6-31 G(d) and 6-311 G(d,p) levels of theory. The static ab initio and DFT calculations showed that the most stable structure is the cyclic form for all cases (n = 3-6). In the ionization of the water trimer, the complex (H 3 O + OH)H 2 O was obtained as a product (complex formation channel). In the larger clusters (n = 4-6), the OH dissociation was only found after the ionization of (H 2 O) n (OH dissociation channel). The OH dissociation occurs via two-step processes: the first step is a proton-transfer process from H 2 O + to H 2 O along the hydrogen bond in the cluster, and then the (H 3 O + OH) complex is formed as a core in the cluster, expressed by (H 2 O + )-H 2 O-H 2 O → (OH)(H 3 O + )-H 2 O. The next step is the second proton-transfer process from H 3 O + OH to the neighboring water molecule, which is expressed by (OH)-H 3 O + -H 2 O → (OH)-H 2 O-H 3 O + . It was found that the OH dissociation takes place immediately after the second proton transfer. The lifetimes of the intermediate complexes are distributed in the range 50-200 fs for n = 4-6. The reaction mechanism was discussed on the basis of theoretical results.

Ab initio linear scaling response theory: electric polarizability by perturbed projection.

A linear scaling method for calculation of the static ab initio response within self-consistent field theory is developed and applied to the calculation of the static electric polarizability. The method is based on the density matrix perturbation theory [Phys. Rev. Lett. 92, 193001 (2004)]], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G(**) level of theory. The locality of the response under a global electric field perturbation is numerically demonstrated by the approximate exponential decay of derivative density matrix elements.

Semi-empirical valence bond models of conjugated alkenes with donor and acceptor substituents

The Heisenberg model is used to describe low-lying states of conjugated alkene ‘bridges’ with donor and/or acceptor substituents. Using a compact set of transferable exchange parameters, each fitted to the ground state ab initio energy of just one molecule, useful semi-empirical energies can be generated for different donor/acceptor combinations and for different chain lengths. A new Hamiltonian is introduced which augments the covalent description with additional parameters for ionic configurations, and for the mixing between covalent and ionic spaces. This leads to useful energies also for higher states. The general approach should be applicable to a wide range of different donor/acceptor/bridge combinations.