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arXiv2009

Absorption and Fluorescence Properties of Oligothiophene Biomarkers from Long-Range-Corrected Time-Dependent Density Functional Theory

The absorption and fluorescence properties in a class of oligothiophene push-pull biomarkers are investigated with a long-range-corrected (LC) density functional method. Using linear response time-dependent density functional theory (TDDFT), we calculate excitation energies, fluorescence energies, oscillator strengths, and excited-state dipole moments. To benchmark and assess the quality of the LC-TDDFT formalism, an extensive comparison is made between LC-BLYP excitation energies and approximate coupled cluster singles and doubles (CC2) calculations. When using a properly-optimized value of the range parameter, "mu", we find that the LC technique provides an accurate description of charge-transfer excitations as a function of biomarker size and chemical functionalization. In contrast, we find that re-optimizing the fraction of Hartree Fock exchange in conventional hybrid functionals still yields an inconsistent description of excitation energies and oscillator strengths for the two lowest excited states in our series of biomarkers. The results of the present study emphasize the importance of a distance-dependent contribution of exchange in TDDFT for investigating excited-state properties.

physics.chem-ph↗

arXiv2009

Physical signatures of discontinuities of the time-dependent exchange-correlation potential

The exact exchange-correlation (XC) potential in time-dependent density-functional theory (TDDFT) is known to develop steps and discontinuities upon change of the particle number in spatially confined regions or isolated subsystems. We demonstrate that the self-interaction corrected adiabatic local-density approximation for the XC potential has this property, using the example of electron loss of a model quantum well system. We then study the influence of the XC potential discontinuity in a real-time simulation of a dissociation process of an asymmetric double quantum well system, and show that it dramatically affects the population of the resulting isolated single quantum wells. This indicates the importance of a proper account of the discontinuities in TDDFT descriptions of ionization, dissociation or charge transfer processes.

cond-mat.mes-hall↗

arXiv2013

Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

physics.chem-ph↗

arXiv2013

Triple-helical collagen hydrogels via covalent aromatic functionalization with 1,3-Phenylenediacetic acid

Chemical crosslinking of collagen is a general strategy to reproduce macroscale tissue properties in physiological environment. However, simultaneous control of protein conformation, material properties and biofunctionality is highly challenging with current synthetic strategies. Consequently, the potentially-diverse clinical applications of collagen-based biomaterials cannot be fully realised. In order to establish defined biomacromolecular systems for mineralised tissue applications, type I collagen was functionalised with 1,3-Phenylenediacetic acid (Ph) and investigated at the molecular, macroscopic and functional levels. Preserved triple helix conformation was observed in obtained covalent networks via ATR-FTIR and WAXS, while network crosslinking degree could be adjusted based on specific reaction conditions. Decreased swelling ratio and increased thermo-mechanical properties were observed compared to state of-the-art carbodiimide (EDC)-crosslinked collagen controls, likely related to the intermolecular covalent incorporation of the aromatic segment. Ph crosslinked hydrogels displayed nearly intact material integrity and only a slight mass decrease following 1-week incubation in either PBS or simulated body fluid (SBF), in contrast to EDC crosslinked collagen. Furthermore, FTIR, SEM and EDS revealed deposition of a calcium-phosphate phase on SBF-retrieved samples, whereby an increased calcium phosphate ratio was observed in hydrogels with higher Ph content. 72-hour material extracts were well tolerated by L929 mouse fibroblasts, whereby cell confluence and metabolic activity (MTS assay) were comparable to those of cells cultured in cell culture medium (positive control). In light of their controlled structure-function properties, these biocompatible collagen hydrogels represent attractive material systems for potential mineralised tissue applications.

physics.chem-ph↗

arXiv2013

Photo-active collagen systems with controlled triple helix architecture

The design of photo-active collagen systems is presented as a basis for establishing biomimetic materials with varied network architecture and programmable macroscopic properties. Following in-house isolation of type I collagen, reaction with vinyl-bearing compounds of varied backbone rigidity, i.e. 4-vinylbenzyl chloride (4VBC) and glycidyl methacrylate (GMA), was carried out. TNBS colorimetric assay, 1H-NMR and ATR-FTIR confirmed covalent and tunable functionalization of collagen lysines. Depending on the type and extent of functionalization, controlled stability and thermal denaturation of triple helices were observed via circular dichroism (CD), whereby the hydrogen-bonding capability of introduced moieties was shown to play a major role. Full gel formation was observed following photo-activation of functionalized collagen solutions. The presence of a covalent network only slightly affected collagen triple helix conformation (as observed by WAXS and ATR-FTIR), confirming the structural organization of functionalized collagen precursors. Photo-activated hydrogels demonstrated an increased denaturation temperature (DSC) with respect to native collagen, suggesting that the formation of the covalent network successfully stabilized collagen triple helices. Moreover, biocompatibility and mechanical competence of obtained hydrogels were successfully demonstrated under physiologically-relevant conditions. These results demonstrate that this novel synthetic approach enabled the formation of biocompatible collagen systems with defined network architecture and programmable macroscopic properties, which can only partially be obtained with current synthetic methods.

physics.chem-ph↗

arXiv2014

Challenging Adiabatic Time-dependent Density Functional Theory with a Hubbard Dimer: The Case of Time-Resolved Long-Range Charge Transfer

We explore an asymmetric two-fermion Hubbard dimer to test the accuracy of the adiabatic approximation of time-dependent density functional theory in modelling time-resolved charge transfer. We show that the model shares essential features of a ground state long-range molecule in real-space, and by applying a resonant field we show that the model also reproduces essential traits of the CT dynamics. The simplicity of the model allows us to propagate with an "adiabatically-exact" approximation, i.e. one that uses the exact ground-state exchange-correlation functional, and compare with the exact propagation. This allows us to study the impact of the time-dependent charge-transfer step feature in the exact correlation potential of real molecules on the resulting dynamics. Tuning the parameters of the dimer allows a study both of charge-transfer between open-shell fragments and between closed-shell fragments. We find that the adiabatically-exact functional is unable to properly transfer charge, even in situations where the adiabatically-exact resonance frequency is remarkably close to the exact resonance, and we analyze why.

physics.chem-ph↗

arXiv2014

Assessment of asymptotically corrected model potential scheme for charge-transfer-like excitations in oligoacenes

We examine the performance of the asymptotically corrected model potential scheme on the two lowest singlet excitation energies of acenes with different number of linearly fused benzene rings (up to 5), employing both the real-time time-dependent density functional theory and the frequency-domain formulation of linear-response time-dependent density functional theory. The results are compared with the experimental data and those calculated by long-range corrected hybrid functionals and others. The long-range corrected hybrid scheme is shown to outperform the asymptotically corrected model potential scheme for charge-transfer-like excitations.

physics.chem-ph↗

arXiv2014

A study of the ice-water interface using the TIP4P/2005 water model

In this work we study the ice-water interface under coexistence conditions by means of molecular simulations using the TIP4P/2005 water model. Following the methodology proposed by Hoyt and co-workers [J. J. Hoyt, M. Asta and A. Karma, Phys. Rev. Lett., 86, 5530, (2001)] we measure the interfacial free energy of ice with liquid water by analysing the spectrum of capillary fluctuations of the interface. We get an orientationally averaged interfacial free energy of 27(2) mN/m, in good agreement with a recent estimate obtained from simulation data of the size of critical clusters [E. Sanz, C. Vega, J. R. Espinosa, R. Caballero-Bernal, J. L. F. Abascal and C. Valeriani, JACS, 135, 15008, (2013)]. We also estimate the interfacial free energy of different planes and obtain 27(2), 28(2)and 28(2) mN/m for the basal, the primary prismatic and the secondary prismatic planes respectively. Finally, we inspect the structure of the interface and find that its thickness is of approximately 4-5 molecular diameters. Moreover, we find that when the basal plane is exposed to the fluid the interface alternates regions of cubic ice with regions of hexagonal ice.

physics.chem-ph↗

arXiv2014

Suppression of Sub-surface Freezing in Free-Standing Thin Films of a Coarse-grained Model of Water

Freezing in the vicinity of water-vapor interfaces is of considerable interest to a wide range of disciplines, most notably the atmospheric sciences. In this work, we use molecular dynamics and two advanced sampling techniques, forward flux sampling and umbrella sampling, to study homogeneous nucleation of ice in free-standing thin films of supercooled water. We use a coarse-grained monoatomic model of water, known as mW, and we find that in this model a vapor-liquid interface suppresses crystallization in its vicinity. This suppression occurs in the vicinity of flat interfaces where no net Laplace pressure in induced. Our free energy calculations reveal that the pre-critical crystalline nuclei that emerge near the interface are thermodynamically less stable than those that emerge in the bulk. We investigate the origin of this instability by computing the average asphericity of nuclei that form in different regions of the film, and observe that average asphericity increases closer to the interface, which is consistent with an increase in the free energy due to increased surface-to-volume ratios.

cond-mat.stat-mech↗

arXiv2014

Developing an aqueous approach for synthesizing Au and M@Au (M = Pd, CuPt) hybrid nanostars with plasmonic properties

Anisotropic Au nanoparticles show unique localized surface plasmon resonance (LSPR) properties, which make it attractive in optical, sensing, and biomedical applications. In this contribution, we report a general and facile strategy towards aqueous synthesis of Au and M@Au (M = Pd, CuPt) hybrid nanostars by reducing HAuCl4 with ethanolamine in the presence of cetyltrimethylammonium bromide (CTAB). According to electron microscopic observation and spectral monitoring, we found that the layered epitaxial growth mode (i.e., Frank-van der Merwe mechanism) contributes to the enlargement of the core, while, the random attachment of Au nanoclusters onto the cores accounts for the formation of the branches. Both of them are indispensable for the formation of the nanostars. The LSPR properties of the Au nanoparticles have been well investigated with morphology control via precursor amount and growth temperature. The Au nanostars showed improved surface-enhanced Raman spectroscopy (SERS) performance for rhodamine 6G due to their sharp edges and tips, which were therefore confirmed as good SERS substrate to detect trace amount of molecules.

physics.chem-ph↗

arXiv2017

Thermodynamic Stability of Driven Open Systems and Control of Phase Separation by Electro-autocatalysis

Motivated by the possibility of electrochemical control of phase separation, a variational theory of thermodynamic stability is developed for driven reactive mixtures, based on a nonlinear generalization of the Cahn-Hilliard and Allen-Cahn equations. The Glansdorff-Prigogine stability criterion is extended for driving chemical work, based on variations of nonequilibrium Gibbs free energy. Linear stability is generally determined by the competition of chemical diffusion and driven autocatalysis. Novel features arise for electrochemical systems, related to controlled total current (galvanostatic operation), concentration-dependent exchange current (Butler-Volmer kinetics), and negative differential reaction resistance (Marcus kinetics). The theory shows how spinodal decomposition can be controlled by solo-autocatalytic charge transfer, with only a single Faradaic reaction. Experimental evidence is presented for intercalation and electrodeposition in rechargeable batteries, and further applications are discussed in solid state ionics, electrovariable optics, electrochemical precipitation, and biological pattern formation.

physics.chem-ph↗

arXiv2018

Photophysics of indole upon x-ray absorption

A photofragmentation study of gas-phase indole (C$_8$H$_7$N) upon single-photon ionization at a photon energy of 420 eV is presented. Indole was primarily inner-shell ionized at its nitrogen and carbon $1s$ orbitals. Electrons and ions were measured in coincidence by means of velocity map imaging. The angular relationship between ionic fragments is discussed along with the possibility to use the angle-resolved coincidence detection to perform experiments on molecules that are strongly oriented in their recoil-frame. The coincident measurement of electrons and ions revealed fragmentation-pathway-dependent electron spectra, linking the structural fragmentation dynamics to different electronic excitations. Evidence for photoelectron-impact self-ionization was observed.

physics.atm-clus↗

arXiv2018

Enhancing radical molecular beams by skimmer cooling

A high-intensity supersonic beam source has been a key component in studies of molecular collisions, molecule-surface interaction, chemical reactions, and precision spectroscopy. However, the molecular density available for experiments in a downstream science chamber is limited by skimmer clogging, which constrains the separation between a valve and a skimmer to at least several hundred nozzle diameters. A recent experiment (Science Advances, 2017, 3, e1602258) has introduced a new strategy to address this challenge: when a skimmer is cooled to a temperature below the freezing point of the carrier gas, skimmer clogging can be effectively suppressed. We go beyond this proof-of-principle work in several key ways. Firstly, we apply the skimmer cooling approach to discharge-produced radical and metastable beams entrained in a carrier gas. We also identify two different processes for skimmer clogging mitigation-shockwave suppression at temperatures around the carrier gas freezing point and diffusive clogging at even lower temperatures. With the carrier clogging removed, we now fully optimize the production of entrained species such as hydroxyl radicals, resulting in a gain of 30 in density over the best commercial devices. The gain arises from both clogging mitigation and favorable geometry with a much shorter valve-skimmer distance.

physics.chem-ph↗

arXiv2018

Reaction Mechanism of the Selective Reduction of CO$_2$ to CO by a Tetraaza [Co$^\text{II}$N$_4$H]$^{2+}$ Complex in the Presence of Protons

The tetraaza [Co$^\text{II}$N$_4$H]$^{2+}$ complex (\textbf{1}) is remarkable for its ability to selectively reduce CO$_2$ to CO with 45\% Faradaic efficiency and a CO to H$_2$ ratio of 3:2. We employ density functional theory (DFT) to determine the reasons behind the unusual catalytic properties of \textbf{1} and the most likely mechanism for CO$_2$ reduction. The selectivity for CO$_2$ over proton reduction is explained by analyzing the catalyst's affinity for the possible ligands present under typical reaction conditions: acetonitrile, water, CO$_2$, and bicarbonate. After reduction of the catalyst by two electrons, formation of [Co$^\text{I}$N$_4$H]$^{+}$-CO$_{2}^{-}$ is strongly favored. Based on thermodynamic and kinetic data, we establish that the only likely route for producing CO from here consists of a protonation step to yield [Co$^\text{I}$N$_4$H]$^{+}$-CO$_{2}$H, followed by reaction with CO$_2$ to form [Co$^\text{II}$N$_4$H]$^{2+}$-CO and bicarbonate. This conclusion corroborates the idea of a direct role of CO$_2$ as a Lewis acid to assist in {C-O} bond dissociation, a conjecture put forward by other authors to explain recent experimental observations. The pathway to formic acid is predicted to be forbidden by high activation barriers, in accordance with the products that are known to be generated by \textbf{1}. Calculated physical observables such as standard reduction potentials and the turnover frequency for our proposed catalytic cycle are in agreement with available experimental data reported in the literature. The mechanism also makes a prediction that may be experimentally verified: that the rate of CO formation should increase linearly with the partial pressure of CO$_2$.

physics.chem-ph↗

arXiv2018

A study of the ozonolysis of isoprene in a cryogenic buffer gas cell by high resolution microwave spectroscopy

We have developed a method to quantify reaction product ratios using high resolution microwave spectroscopy in a cryogenic buffer gas cell. We demonstrate the power of this method with the study of the ozonolysis of isoprene, CH2=C(CH3)-CH=CH2, the most abundant, non-methane hydrocarbon emitted into the atmosphere by vegetation. Isoprene is an asymmetric diene, and reacts with O3 at the 1,2 position to produce methyl vinyl ketone (MVK), formaldehyde, and a pair of carbonyl oxides: [CH3CO-CH=CH2 + CH2=OO] + [CH2=O + CH3COO-CH=CH2]. Alternatively, O3 could attack at the 3,4 position to produce methacrolein (MACR), formaldehyde, and two carbonyl oxides [CH2=C(CH3)-CHO + CH2=OO] + [CH2=O + CH2=C(CH3)-CHOO]. Purified O3 and isoprene were mixed for approximately 10 seconds under dilute (1.5-4% in argon) continuous flow conditions in an alumina tube held at 298 K and 5 Torr. Products exiting the tube were rapidly slowed and cooled within the buffer gas cell by collisions with cryogenic (4-7 K) He. High resolution chirped pulse microwave detection between 12 and 26 GHz was used to achieve highly sensitive (ppb scale), isomer-specific product quantification. We observed a ratio of MACR to MVK of 2.1 +/- 0.4 under 1:1 ozone to isoprene conditions and 2.1 +/- 0.2 under 2:1 ozone to isoprene conditions, a finding which is consistent with previous experimental results. Additionally, we discuss relative quantities of formic acid (HCOOH), an isomer of CH2=OO, and formaldehyde (CH2=O) under varying experimental conditions, and characterize the spectroscopic parameters of the singly-substituted 13C trans-isoprene and 13C anti-periplanar-methacrolein species. This work has the potential to be extended towards a complete branching ratio analysis, as well towards the ability to isolate, identify, and quantify new reactive intermediates in the ozonolysis of alkenes.

physics.chem-ph↗

arXiv2018

Developing effective electronic-only coupled-cluster and Muller-Plesset perturbation theories for the muonic molecules

Recently we have proposed an effective Hartree-Fock (EHF) theory for the electrons of the muonic molecules that is formally equivalent to the HF theory within the context of the Nuclear-Electronic Orbital theory [Phys. Chem. Chem. Phys. 20, 4466 (2018)]. In the present report we extend the muon-specific effective electronic structure theory beyond the EHF level by introducing the effective second order Muller-Plesset perturbation theory (EMP2) and the effective coupled-cluster theory at single and double excitation levels (ECCSD) as well as an improved version including perturbative triple excitations (ECCSD(T)). These theories incorporate electron-electron correlation into the effective paradigm and through their computational implementation, a diverse set of small muonic species is considered as a benchmark at these post-EHF levels. A comparative computational study on this set demonstrates that the muonic bond length is in general non-negligibly longer than corresponding hydrogenic analogs. Next, the developed post-EHF theories are applied for the muoniated N-Heterocyclic carbene/silylene/germylene and the muoniated triazolium cation revealing the relative stability of the sticking sites of the muon in each species. The computational results, in line with previously reported experimental data demonstrate that the muon generally prefers to attach to the divalent atom with carbeneic nature. A detailed comparison of these muonic adducts with the corresponding hydrogenic adducts reveals subtle differences that have already been overlooked.

physics.atm-clus↗

arXiv2018

Electronic structure and rovibrational predissociation of the 2sPi state in KLi

Adiabatic potential energy curves of the 3sSigma+, 3tSigma+, 2sPi and 2tPi states correlating for large internuclear distance with the K(4s) + Li(2p) atomic asymptote were calculated. Very good agreement between the calculated and the experimental curve of the 2sPi state allowed for a reliable description of the dissociation process through a small (20 cm-1 for J = 0) potential energy barrier. The barrier supports several rovibrational quasi-bound states and explicit time evolution of these states via the time-dependent nuclear Schroedinger equation, showed that the state populations decay exponentially in time. We were able to precisely describe the time-dependent dissociation process of several rovibrational levels and found that our calculated spectrum match very well with the assigned experimental spectrum. Moreover, our approach is able to predict the positions of previously unassigned lines despite their low intensity

physics.chem-ph↗

arXiv2017

Sampling the protonation states: pH-dependent UV absorption spectrum of a polypeptide dyad

When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, aimed at sampling both the phase space and protonation state space of a short polypeptide featuring a tyrosine--tryptophan dyad interacting with two aspartic acid residues. We show that such a protocol is accurate enough to reproduce the tyrosine UV absorption spectrum at both acidic and basic pH. Moreover, it is confirmed that UV-induced radical tryptophan is reduced thanks to an electron transfer from tyrosine, ultimately explaining the complex pH-dependent behavior of the peptide spectrum.

physics.chem-ph↗