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arXiv2014

Renormalization of myoglobin-ligand binding energetics by quantum many-body effects

We carry out a first-principles atomistic study of the electronic mechanisms of ligand binding and discrimination in the myoglobin protein. Electronic correlation effects are taken into account using one of the most advanced methods currently available, namely a linear-scaling density functional theory (DFT) approach wherein the treatment of localized iron 3d electrons is further refined using dynamical mean-field theory (DMFT). This combination of methods explicitly accounts for dynamical and multi-reference quantum physics, such as valence and spin fluctuations, of the 3d electrons, whilst treating a significant proportion of the protein (more than 1000 atoms) with density functional theory. The computed electronic structure of the myoglobin complexes and the nature of the Fe-O2 bonding are validated against experimental spectroscopic observables. We elucidate and solve a long standing problem related to the quantum-mechanical description of the respiration process, namely that DFT calculations predict a strong imbalance between O2 and CO binding, favoring the latter to an unphysically large extent. We show that the explicit inclusion of many body-effects induced by the Hund's coupling mechanism results in the correct prediction of similar binding energies for oxy- and carbonmonoxymyoglobin.

physics.chem-ph↗

arXiv2014

Understanding shape entropy through local dense packing

Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals has been demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. Here, we show quantitatively that shape drives the phase behavior of systems of anisotropic particles upon crowding through DEFs. We define DEFs in generic systems, and compute them for several hard particle systems. We show that they are on the order of a few kT at the onset of ordering, placing DEFs on par with traditional depletion, van der Waals, and other intrinsic interactions. In experimental systems with these other interactions, we provide direct quantitative evidence that entropic effects of shape also contribute to self-assembly. We use DEFs to draw a distinction between self-assembly and packing behavior. We show that the mechanism that generates directional entropic forces is the maximization of entropy by optimizing local particle packing. We show that this mechanism occurs in a wide class of systems, and we treat, in a unified way, the entropy-driven phase behavior of arbitrary shapes incorporating the well-known works of Kirkwood, Onsager, and Asakura and Oosawa.

cond-mat.soft↗

arXiv2017

Allocating dissipation across a molecular machine cycle to maximize flux

Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing a fixed free energy budget. Since evolution is expected to favor rapid-turnover machines that operate efficiently, we investigate how this free energy budget can be allocated to maximize flux. Unconstrained optimization eliminates intermediate metastable states, indicating that flux is enhanced in molecular machines with fewer states. When maintaining a set number of states, we show that---in contrast to previous findings---the flux-maximizing allocation of dissipation is not even. This result is consistent with the coexistence of both `irreversible' and reversible transitions in molecular machine models that successfully describe experimental data, which suggests that in evolved machines different transitions differ significantly in their dissipation.

cond-mat.stat-mech↗

arXiv2018

Mid-infrared feed-forward dual-comb spectroscopy at 3 $μ$m

Mid-infrared high-resolution spectroscopy has proven an invaluable tool for the study of the structure and dynamics of molecules in the gas phase. The advent of frequency combs advances the frontiers of precise molecular spectroscopy. Here we demonstrate, in the important 3-μm spectral region of the fundamental CH stretch in molecules, dual-comb spectroscopy with experimental coherence times between the combs that exceed half-an-hour. Mid-infrared Fourier transform spectroscopy using two frequency combs with self-calibration of the frequency scale, negligible contribution of the instrumental line-shape to the spectral profiles, high signal-to-noise ratio and broad spectral bandwidth opens up novel opportunities for precision spectroscopy of small molecules. Highly multiplexed metrology of line shapes may be envisioned.

physics.optics↗

arXiv2013

Singlet Excited States of Anions with Higher Main Group Elements

Previous studies have shown that dipole-bound excited states exist for certain small anions. However, valence excited states have been reported for some closed-shell anions, but those with singlet valence excited states have, thus far, contained a single silicon atom. This work utilizes high-level coupled cluster theory previously shown to reproduce excited state energies to better than 0.1 eV compared with experiment in order to examine the electronic excited state properties of anions containing silicon and other higher main group atoms as well as their first row analogues. Of the fourteen anions involved in this study, nine possess bound excited states of some kind: CH$_2$SN$^-$, C$_3$H$^-$, CCSiH$^-$, CCSH$^-$, CCNH$_2^-$, CCPH$_2^-$, BH$_3$PH$_2^-$, AlH$_3$NH$_2^-$, and AlH$_3$PH$_2^-$. Two possess clear valence states: CCSiH$^-$ and its first row analogue C$_3$H$^-$. Substantial mixing appears to be present in the valence and dipole-bound characters for the first excited state wavefunctions of many of the systems reporting excited states, but the mixing is most pronounced with the ammonia borane-like AlH$_3$NH$_2^-$, and AlH$_3$PH$_2^-$ anions. Inclusion of second row atoms in anions whose corresponding radical is strongly dipolar increases the likelihood for the existence of excited states of any kind, but among the systems considered to date with this methodology, only the nature of group 14 atoms in small, closed-shell anions has yet been shown to allow valence singlet excited states.

physics.chem-ph↗

arXiv2013

Analysis of double hybrid density-functionals along the adiabatic connection

We present a graphical analysis of the adiabatic connections underlying double-hybrid density-functional methods that employ second-order perturbation theory. Approximate adiabatic connection formulae relevant to the construction of these functionals are derived and compared directly with those calculated using accurate ab initio methods. The discontinuous nature of the approximate adiabatic integrands is emphasized, the discontinuities occurring at interaction strengths which mark the transitions between regions that are: (i) described predominantly by second- order perturbation theory (ii) described by a mixture of density-functional and second-order perturbation theory contributions and (iii) described purely by density-functional theory. Numerical examples are presented for a selection of small molecular systems and van der Waals dimers. The impacts of commonly used approximations in each of the three sections of the adiabatic connection are discussed along with possible routes for the development of improved double-hybrid methodologies.

physics.chem-ph↗

arXiv2013

Interatomic potentials, electric properties, and spectroscopy of the ground and excited states of the Rb_2 molecule: Ab initio calculations and effect of a non-resonant field

We formulate the theory for a diatomic molecule in a spatially degenerate electronic state interacting with a non-resonant laser field and investigate its rovibrational structure in the presence of the field. We report on \textit{ab initio} calculations employing the double electron attachment intermediate Hamiltonian Fock space coupled cluster method restricted to single and double excitations for all electronic states of the Rb$_2$ molecule up to $5s+5d$ dissociation limit of about 26.000$\,$cm$^{-1}$. In order to correctly predict the spectroscopic behavior of Rb$_2$, we have also calculated the electric transition dipole moments, non-adiabatic coupling and spin-orbit coupling matrix elements, and static dipole polarizabilities, using the multireference configuration interaction method. When a molecule is exposed to strong non-resonant light, its rovibrational levels get hybridized. We study the spectroscopic signatures of this effect for transitions between the X$^1Σ_g^+$ electronic ground state and the A$^1Σ_u^+$ and b$^3Π_u$ excited state manifold. The latter is characterized by strong perturbations due to the spin-orbit interaction. We find that for non-resonant field strengths of the order $10^9$W/cm$^2$, the spin-orbit interaction and coupling to the non-resonant field become comparable. The non-resonant field can then be used to control the singlet-triplet character of a rovibrational level.

physics.atom-ph↗

arXiv2013

Optical Kerr and Cotton-Mouton effects in atomic gases: a quantum-statistical study

Theory of the birefringence of the refractive index in atomic diamagnetic dilute gases in the presence of static electric (optical Kerr effect) and magnetic (Cotton-Mouton effect) fields is formulated. Quantum-statistical expressions for the second Kerr and Cotton-Mouton virial coefficients, valid both in the low and high temperature regimes, are derived. It is shown that both virial coefficients can rigorously be related to the difference of the fourth derivatives of the thermodynamic (pressure) virial coefficient with respect to the strength of the non-resonant optical fields with parallel and perpendicular polarizations and with respect to the external static (electric or magnetic) field. Semiclassical expansions of the Kerr and Cotton-Mouton coefficients are also considered, and quantum corrections up to and including the second order are derived. Calculations of the second Kerr and Cotton-Mouton virial coefficients of the helium-4 gas at various temperatures are reported. The role of the quantum-mechanical effects and the convergence properties of the semiclassical expansions are discussed. Theoretical results are compared with the available experimental data.

physics.atom-ph↗

arXiv2013

Hamiltonian replica-exchange in GROMACS: a flexible implementation

A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field corrections.

physics.comp-ph↗

arXiv2013

VUV Spectroscopic Study of the BB" 1Su+ State of H2

Spectral lines, probing rotational quantum states J'=0,1,2 of the inner well vibrations (v' =< 8) in the BB" 1Su+ state of molecular hydrogen, were recorded in high resolution using a vacuum ultraviolet (VUV) Fourier transform absorption spectrometer in the wavelength range 73-86 nm. Accurate line positions and predissociation widths are determined from a fit to the absorption spectra. Improved values for the line positions are obtained, while the predissociation widths agree well with previous investigations.

physics.chem-ph↗

arXiv2014

Characterizing a configuration interaction excited state using natural transition geminals

We introduce natural transition geminals as a means to qualitatively understand a transition where double excitations are important. The first two $A_{1}$ singlet states of the CH cation are used as an initial example. We calculate these states with configuration interaction singles (CIS) and state-averaged Monte Carlo configuration interaction (SA-MCCI). For each method we compare the important natural transition geminals with the dominant natural transition orbitals. We then compare SA-MCCI and full configuration interaction (FCI) with regards to the natural transition geminals using the beryllium atom. We compare using the natural transition geminals with analyzing the important configurations in the CI expansion to give the dominant transition for the beryllium atom and the carbon dimer. Finally we calculate the natural transition geminals for two electronic excitations of formamide.

physics.chem-ph↗

arXiv2013

Linear-scaling and parallelizable algorithms for stochastic quantum chemistry

For many decades, quantum chemical method development has been dominated by algorithms which involve increasingly complex series of tensor contractions over one-electron orbital spaces. Procedures for their derivation and implementation have evolved to require the minimum amount of logic and rely heavily on computationally efficient library-based matrix algebra and optimized paging schemes. In this regard, the recent development of exact stochastic quantum chemical algorithms to reduce computational scaling and memory overhead requires a contrasting algorithmic philosophy, but one which when implemented efficiently can often achieve higher accuracy/cost ratios with small random errors. Additionally, they can exploit the continuing trend for massive parallelization which hinders the progress of deterministic high-level quantum chemical algorithms. In the Quantum Monte Carlo community, stochastic algorithms are ubiquitous but the discrete Fock space of quantum chemical methods is often unfamiliar, and the methods introduce new concepts required for algorithmic efficiency. In this paper, we explore these concepts and detail an algorithm used for Full Configuration Interaction Quantum Monte Carlo (FCIQMC), which is implemented and available in MOLPRO and as a standalone code, and is designed for high-level parallelism and linear-scaling with walker number. Many of the algorithms are also in use in, or can be transferred to, other stochastic quantum chemical methods and implementations. We apply these algorithms to the strongly correlated Chromium dimer, to demonstrate their efficiency and parallelism.

physics.comp-ph↗

arXiv2014

Hydration of Clays at the Molecular Scale: The Promising Perspective of Classical Density Functional Theory

We report here how the hydration of complex surfaces can be efficiently studied thanks to recent advances in classical molecular density functional theory. This is illustrated on the example of the pyrophylite clay. After presenting the most recent advances, we show that the strength of this implicit method is that (i) it is in quantitative or semi-quantitative agreement with reference all-atoms simulations (molecular dynamics here) for both the solvation structure and energetics, and that (ii) the computational cost is two to three orders of magnitude less than in explicit methods. The method remains imperfect, in that it locally overestimates the polarization of water close to hydrophylic sites of the clay. The high numerical efficiency of the method is illustrated and exploited to carry a systematic study of the electrostatic and van der Waals components of the surface-solvant interactions within the most popular force field for clays, CLAYFF. Hydration structure and energetics are found to weakly depend upon the electrostatics. We conclude on the consequences of such findings in future force-field development.

physics.chem-ph↗

arXiv2018

On the accuracy of retinal protonated Schiff base models

We investigate the molecular geometries of the ground state and the minimal energy conical intersections (MECIs) between the ground and first excited states of the models for the retinal protonated Schiff base in the gas phase using the extended multistate complete active space second-order perturbation theory (XMS-CASPT2). The biggest model in this work is the rhodopsin chromophore truncated between the ε and δ carbon atoms, which consists of 54 atoms and 12-orbital π conjugation. The results are compared with those obtained by the state-averaged complete active space self-consistent field (SA-CASSCF). The XMS-CASPT2 results suggest that the minimum energy conical intersection associated with the so-called 13-14 isomerization is thermally inaccessible, which is in contrast to the SA-CASSCF results. The differences between the geometries of the conical intersections computed by SA-CASSCF and XMS-CASPT2 are ascribed to the fact that the charge transfer states are more stabilized by dynamical electron correlation than the diradicaloid states. The impact of the various choices of active spaces, basis sets, and state averaging schemes is also examined.

physics.chem-ph↗

arXiv2018

A Simple Model For Scalar Relativistic Corrections To Molecular Total Atomization Energies

Scalar relativistic corrections to atomization energies of 1st-and 2nd-row molecules can be rationalized in terms of a simple additive model, linear in changes in atomic s populations. In a sample of 200 first-and second-row molecules, such a model can account for over 98% of the variance (99% for the first-row subset). The remaining error can be halved again by adding a term involving the change in atomic p populations: those coefficients need not be fitted but can be fixed from atomic electron affinity calculations. This model allows a fairly accurate a priori estimate for the importance of scalar relativistic corrections on a reaction energy, at essentially zero computational cost. While this is not a substitute for explicit calculation of Douglas-Kroll-Hess (DKH) or exact two-component (X2C) relativistic corrections, the model offers an interpretative tool for the chemical analysis of scalar relativistic contributions to reaction energies.

physics.chem-ph↗

arXiv2018

Cross sections for electron collision with pyridine [C$_{5}$H$_{5}$N] molecule

The absolute grand-total cross section (TCS) for electron scattering from pyridine, C$_{5}$H$_{5}$N, molecules has been measured at impact energies from 0.6 to 300 eV in the linear electron-transmission experiment. The obtained TCS energy dependence appears to be typical for targets of high electric dipole moment; the cross section generally decreases with rising energy, except for the 3-20 eV range, where a broad enhancement peaked near 8.5 eV is clearly visible. Below 10 eV, some weak structures which can be attributed to resonant scattering processes are also discernible. The present TCS energy dependence is compared with TCS experimental data obtained recently for energies above 13 eV by Traore Dubuis et al. [26]. The TCS for pyridine has been confronted with TCS for benzene to search how the replacement of the CH group in the benzene ring with the nitrogen atom influences the electron scattering process. In addition, for pyridine and its halogenated derivatives: 2-chloropyridine [2-C$_{5}$H$_{4}$ClN] and 2-bromopyridine [2-C$_{5}$H$_{4}$BrN], integral elastic (ECS) and ionization (ICS) cross sections have been calculated at intermediate and high electron-impact energies within semiempirical approaches. For pyridine the sum of ECS and ICS is in reasonable agreement with the measured TCS above 40 eV.

physics.chem-ph↗

arXiv2018

Pre-Born-Oppenheimer Molecular Structure Theory

In pre-Born-Oppenheimer (pre-BO) theory a molecule is considered as a quantum system as a whole, including the electrons and the atomic nuclei on the same footing. This approach is fundamentally different from the traditional quantum chemistry treatment, which relies on the separation of the motion of the electrons and the atomic nuclei. A fully quantum mechanical treatment of molecules has a great promise for future developments and applications. Its most accurate versions may contribute to the definition of new schemes for metrology and testing fundamental physical theories; its approximate versions can provide an efficient theoretical description for molecule-positron interactions and, in general, it would circumvent the tedious computation and fitting of potential energy surfaces and non-adiabatic coupling vectors. To achieve these goals, the review points out important technical and fundamental open questions. Most interestingly, the reconciliation of pre-BO theory with the classical chemistry knowledge touches upon fundamental problems related to the measurement problem of quantum mechanics.

physics.chem-ph↗

arXiv2018

Gas phase detection and rotational spectroscopy of ethynethiol, HCCSH

We report the gas-phase detection and spectroscopic characterization of ethynethiol ($\mathrm{HCCSH}$), a metastable isomer of thioketene ($\mathrm{H_2C_2S}$) using a combination of Fourier-transform microwave and submillimeter-wave spectroscopies. Several $a$-type transitions of the normal species were initially detected below 40 GHz using a supersonic expansion-electrical discharge source, and subsequent measurement of higher-frequency, $b$-type lines using double resonance provided accurate predictions in the submillimeter region. With these, searches using a millimeter-wave absorption spectrometer equipped with a radio frequency discharge source were conducted in the range 280 - 660 GHz, ultimately yielding nearly 100 transitions up to $^rR_0(36)$ and $^rQ_0(68)$. From the combined data set, all three rotational constants and centrifugal distortion terms up to the sextic order were determined to high accuracy, providing a reliable set of frequency predictions to the lower end of the THz band. Isotopic substitution has enabled both a determination of the molecular structure of $\mathrm{HCCSH}$ and, by inference, its formation pathway in our nozzle discharge source via the bimolecular radical-radical recombination reaction $\mathrm{SH + C_2H}$, which is calculated to be highly exothermic (-477 kJ/mol) using the HEAT345(Q) thermochemical scheme.

astro-ph.GA↗