Quantum dynamics in complex systems: from spectroscopy to electron transport

Desde sus comienzos, la espectroscopia ha jugado un rol fundamental en nuestra comprensiónde la estructura electrónica de la materia. Sin embargo, el modelado teórico depropiedades ópticas representa todavía un enorme desafío; los métodos mas robustos enla descripción de estados excitados suelen ser computacionalmente prohibitivos mientrasque las predicciones arrojadas por las técnicas mas accesibles con frecuencia se encuentranmuy alejadas de los valores experimentales. En este escenario, como pieza fundamentaldel presente trabajo de tesis se desarrolló una novedosa implementación de la teoríadel funcional de la densidad dependiente del tiempo (TDDFT) incluyendo efectos delentorno molecular a través de un Hamiltoniano híbrido cuántico-clásico (QM-MM). Estaimplementación se realizó en el marco del programa de código libre LIO; la herramientaomnipresente a lo largo de esta tesis. La descripción propuesta permitió la reproduccióncuantitativa de resultados espectroscópicos de sistemas moleculares inmersos en entornosdiversos como matrices proteicas o solventes de distinta naturaleza. Asimismo, seanalizaron las ventajas computacionales asociadas a diferentes niveles de paralelizacióndel código y en particular, a la migración parcial del cómputo a placas de procesamientográfico (GPU). El esquema presentado resultó una herramienta fundamental en laelucidación de mecanismos de reacción de relevancia fisiológica entre especies derivadasde dos importantes moléculas se~nalizadoras como el ácido sulfhídrico (H2S) y el óxidonítrico (NO). La formulación implementada durante la primer parte de esta tesis fue modificadaposteriormente para permitir el tratamiento de sistemas cuánticos abiertos con el objetivode estudiar el fenómeno de transporte electrónico molecular. Este proceso subyacente atoda la química redox ha despertado gran interés a lo largo de la historia. En particular,en las últimas dos décadas el potencial de las moléculas como componentes electrónicosen miniatura ha causado un enorme revuelo en las comunidades científica, tecnológicae industrial. A diferencia de las aproximaciones tradicionales, basadas típicamente enel formalismo de funciones de Green de no equilibrio (NEGF) en combinación con lateoría del funcional de la densidad (DFT), el esquema presentado permite la descripciónde estados no estacionarios abriendo las puertas al estudio de efectos transientes oacoplamientos con campos externos dependientes del tiempo. Esta metodología |cuyocosto computacional es comparable al de un cálculo TDDFT estándar| es, hastael alcance de nuestro conocimiento, la primer implementación ab-initio de este tiporeportada en la literatura. De esta manera, el modelo propuesto fue sometido a unarigurosa validación estudiando la conductividad de hidrocarburos saturados e insaturadosy contrastando con valores provenientes de distintos formalismos.Since its beginnings, spectroscopy has played a key role in our understanding of theelectronic structure of matter. However, the theoretical modeling of optical propertiesstill represents a great challenge; the most robust techniques in the description of excitedstates are often computationally prohibitive whereas the predictions obtained from themost accessible methods are usually far from the experimental values. In this scenario, asa cornerstone of the present thesis a novel implementation of the time dependent densityfunctional theory (TD-DFT) including effects of the molecular environment through anhybrid quantum-classical Hamiltonian (QM-MM) was developed. This implementationwas performed in the context of the LIO free software; the omnipresent tool throughoutthis work. The presented description allowed the spectroscopic signature reproductionof molecular systems immersed in complex environments such as protein matrices ordifferent solvents with quantitative accuracy. Additionally, the computational advantagesassociated with different levels of parallelization and in particular with the partialmigration of the computation to graphics processing units (GPU) were analyzed. Thepresented scheme was a fundamental tool in the elucidation of physiologically relevantreaction mechanisms between species derived from two important signaling moleculessuch as hydrogen sulfide (H2S) and nitric oxide (NO). The formulation implemented during the first part of this thesis was modified to allowthe treatment of open quantum systems with the aim of studying the phenomenon ofelectron transport through molecules. This process, that underlies all redox chemistry,has aroused great interest throughout the history. In particular, during the last twodecades the potential of molecules as miniature electronic components has been a majorfocus of attention for the scientific, technological and industrial communities. Unlikethe standard approaches for calculating these properties, typically based on the nonequilibrium Green's functions (NEGF) formalism in combination with density functionaltheory (DFT), the scheme presented in this thesis allows the description of non-stationarystates opening the door to the study of a great variety of transient effects or the couplingwith time-dependent external fields. This methodology |whose computational cost iscomparable to a standard TDDFT calculation| is, to the best of our knowledge, the firstab-initio implementation of this kind reported in the literature. Therefore, the proposedmodel was subjected to a rigorous validation by studying the conductivity of saturatedand unsaturated hydrocarbons and contrasting the results with different formalisms.Fil: Morzan, Uriel Nicolás. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Physical Review X 8, 031061 (2018)] have revealed the presence of a pronounced mode at $\sim$0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2$\sigma$) from such collective behavior, illustrating how specific THz vibrational modes can be triggered through optical excitations and other charge reorganization processes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can induce a multiscale response involving the two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fr\"ohlich condensates that are fundamentally determined by nonlinear interactions in biology.Comment: 47 pages in total: consisting of 43 of main manuscipt and 4 pages of supporting informatio

Electron dynamics in complex environments with real-time time dependent density functional theory in a QM-MM framework

This article presents a time dependent density functional theory (TDDFT) implementation to propagate the Kohn-Sham equations in real time, including the effects of a molecular environment through a Quantum-Mechanics Molecular-Mechanics (QM-MM) hamiltonian. The code delivers an all-electron description employing Gaussian basis functions, and incorporates the Amber force-field in the QM-MM treatment. The most expensive parts of the computation, comprising the commutators between the hamiltonian and the density matrix—required to propagate the electron dynamics—, and the evaluation of the exchange-correlation energy, were migrated to the CUDA platform to run on graphics processing units, which remarkably accelerates the performance of the code. The method was validated by reproducing linear-response TDDFT results for the absorption spectra of several molecular species. Two different schemes were tested to propagate the quantum dynamics: (i) a leap-frog Verlet algorithm, and (ii) the Magnus expansion to first-order. These two approaches were confronted, to find that the Magnus scheme is more efficient by a factor of six in small molecules. Interestingly, the presence of iron was found to seriously limitate the length of the integration time step, due to the high frequencies associated with the core-electrons. This highlights the importance of pseudopotentials to alleviate the cost of the propagation of the inner states when heavy nuclei are present. Finally, the methodology was applied to investigate the shifts induced by the chemical environment on the most intense UV absorption bands of two model systems of general relevance: the formamide molecule in water solution, and the carboxy-heme group in Flavohemoglobin. In both cases, shifts of several nanometers are observed, consistently with the available experimental data.Fil: Morzan, Uriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; ArgentinaFil: Ramírez, Francisco Fernando. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; ArgentinaFil: Oviedo, María Belén. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Sanchez, Cristian Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Scherlis Perel, Damian Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Inorgánica, Analítica y Química Física; ArgentinaFil: González Lebrero, Mariano Camilo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Química y Físico-Química Biológicas "Prof. Alejandro C. Paladini". Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Química y Físico-Química Biológicas; Argentin

The collective burst mechanism of angular jumps in liquid water

Understanding the microscopic origins of collective reorientational motions in aqueous systems requires techniques that allow us to reach beyond our chemical imagination. Herein, we elucidate a mechanism using a protocol that automatically detects abrupt motions in reorientational dynamics, showing that large angular jumps in liquid water involve highly cooperative orchestrated motions. Our automatized detection of angular fluctuations, unravels a heterogeneity in the type of angular jumps occurring concertedly in the system. We show that large orientational motions require a highly collective dynamical process involving correlated motion of many water molecules in the hydrogen-bond network that form spatially connected clusters going beyond the local angular jump mechanism. This phenomenon is rooted in the collective fluctuations of the network topology which results in the creation of defects in waves on the THz timescale. The mechanism we propose involves a cascade of hydrogen-bond fluctuations underlying angular jumps and provides new insights into the current localized picture of angular jumps, and its wide use in the interpretations of numerous spectroscopies as well in reorientational dynamics of water near biological and inorganic systems. The role of finite size effects, as well as of the chosen water model, on the collective reorientation is also elucidated

Vibronic Dynamics of Photodissociating ICN from Simulations of Ultrafast X-Ray Absorption Spectroscopy

Ultrafast UV-pump/soft-X-ray-probe spectroscopy is a subject of great interest since it can provide detailed information about dynamical photochemical processes with ultrafast resolution and atomic specificity. Here, we focus on the photodissociation of ICN in the 1Π1 excited state, with emphasis on the transient response in the soft-X-ray spectral region as described by the ab initio spectral lineshape averaged over the nuclear wavepacket probability density. We find that the carbon K-edge spectral region reveals a rich transient response that provides direct insights into the dynamics of frontier orbitals during the I−CN bond cleavage process. The simulated UV-pump/soft-X-ray-probe spectra exhibit detailed dynamical information, including a time-domain signature for coherent vibration associated with the photogenerated CN fragment. © 2020 The Authors. Published by Wiley-VCH Gmb

Eigenvector Centrality Distribution for Characterization of Protein Allosteric Pathways

Determining the principal energy pathways for allosteric communication in biomolecules, that occur as a result of thermal motion, remains challenging due to the intrinsic complexity of the systems involved. Graph theory provides an approach for making sense of such complexity, where allosteric proteins can be represented as networks of amino acids. In this work, we establish the eigenvector centrality metric in terms of the mutual information, as a mean of elucidating the allosteric mechanism that regulates the enzymatic activity of proteins. Moreover, we propose a strategy to characterize the range of the physical interactions that underlie the allosteric process. In particular, the well known enzyme, imidazol glycerol phosphate synthase (IGPS), is utilized to test the proposed methodology. The eigenvector centrality measurement successfully describes the allosteric pathways of IGPS, and allows to pinpoint key amino acids in terms of their relevance in the momentum transfer process. The resulting insight can be utilized for refining the control of IGPS activity, widening the scope for its engineering. Furthermore, we propose a new centrality metric quantifying the relevance of the surroundings of each residue. In addition, the proposed technique is validated against experimental solution NMR measurements yielding fully consistent results. Overall, the methodologies proposed in the present work constitute a powerful and cost effective strategy to gain insight on the allosteric mechanism of proteins

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.Recent experimental evidence shows a new type of intrinsic fluorescence in biomolecules void of aromatic chemical compounds whose origin is unclear. Here, the authors use non-adiabatic AIMD simulations to show a potential carbonyl-lock mechanism originating this phenomenon

Short hydrogen bonds enhance nonaromatic protein-related fluorescence.

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications

Short hydrogen bonds enhance nonaromatic protein-related fluorescence.

Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications

Quantum dynamics in complex systems: from spectroscopy to electron transport

Desde sus comienzos, la espectroscopia ha jugado un rol fundamental en nuestra comprensiónde la estructura electrónica de la materia. Sin embargo, el modelado teórico depropiedades ópticas representa todavía un enorme desafío; los métodos mas robustos enla descripción de estados excitados suelen ser computacionalmente prohibitivos mientrasque las predicciones arrojadas por las técnicas mas accesibles con frecuencia se encuentranmuy alejadas de los valores experimentales. En este escenario, como pieza fundamentaldel presente trabajo de tesis se desarrolló una novedosa implementación de la teoríadel funcional de la densidad dependiente del tiempo (TDDFT) incluyendo efectos delentorno molecular a través de un Hamiltoniano híbrido cuántico-clásico (QM-MM). Estaimplementación se realizó en el marco del programa de código libre LIO; la herramientaomnipresente a lo largo de esta tesis. La descripción propuesta permitió la reproduccióncuantitativa de resultados espectroscópicos de sistemas moleculares inmersos en entornosdiversos como matrices proteicas o solventes de distinta naturaleza. Asimismo, seanalizaron las ventajas computacionales asociadas a diferentes niveles de paralelizacióndel código y en particular, a la migración parcial del cómputo a placas de procesamientográfico (GPU). El esquema presentado resultó una herramienta fundamental en laelucidación de mecanismos de reacción de relevancia fisiológica entre especies derivadasde dos importantes moléculas se~nalizadoras como el ácido sulfhídrico (H2S) y el óxidonítrico (NO). La formulación implementada durante la primer parte de esta tesis fue modificadaposteriormente para permitir el tratamiento de sistemas cuánticos abiertos con el objetivode estudiar el fenómeno de transporte electrónico molecular. Este proceso subyacente atoda la química redox ha despertado gran interés a lo largo de la historia. En particular,en las últimas dos décadas el potencial de las moléculas como componentes electrónicosen miniatura ha causado un enorme revuelo en las comunidades científica, tecnológicae industrial. A diferencia de las aproximaciones tradicionales, basadas típicamente enel formalismo de funciones de Green de no equilibrio (NEGF) en combinación con lateoría del funcional de la densidad (DFT), el esquema presentado permite la descripciónde estados no estacionarios abriendo las puertas al estudio de efectos transientes oacoplamientos con campos externos dependientes del tiempo. Esta metodología |cuyocosto computacional es comparable al de un cálculo TDDFT estándar| es, hastael alcance de nuestro conocimiento, la primer implementación ab-initio de este tiporeportada en la literatura. De esta manera, el modelo propuesto fue sometido a unarigurosa validación estudiando la conductividad de hidrocarburos saturados e insaturadosy contrastando con valores provenientes de distintos formalismos.Since its beginnings, spectroscopy has played a key role in our understanding of theelectronic structure of matter. However, the theoretical modeling of optical propertiesstill represents a great challenge; the most robust techniques in the description of excitedstates are often computationally prohibitive whereas the predictions obtained from themost accessible methods are usually far from the experimental values. In this scenario, asa cornerstone of the present thesis a novel implementation of the time dependent densityfunctional theory (TD-DFT) including effects of the molecular environment through anhybrid quantum-classical Hamiltonian (QM-MM) was developed. This implementationwas performed in the context of the LIO free software; the omnipresent tool throughoutthis work. The presented description allowed the spectroscopic signature reproductionof molecular systems immersed in complex environments such as protein matrices ordifferent solvents with quantitative accuracy. Additionally, the computational advantagesassociated with different levels of parallelization and in particular with the partialmigration of the computation to graphics processing units (GPU) were analyzed. Thepresented scheme was a fundamental tool in the elucidation of physiologically relevantreaction mechanisms between species derived from two important signaling moleculessuch as hydrogen sulfide (H2S) and nitric oxide (NO). The formulation implemented during the first part of this thesis was modified to allowthe treatment of open quantum systems with the aim of studying the phenomenon ofelectron transport through molecules. This process, that underlies all redox chemistry,has aroused great interest throughout the history. In particular, during the last twodecades the potential of molecules as miniature electronic components has been a majorfocus of attention for the scientific, technological and industrial communities. Unlikethe standard approaches for calculating these properties, typically based on the nonequilibrium Green's functions (NEGF) formalism in combination with density functionaltheory (DFT), the scheme presented in this thesis allows the description of non-stationarystates opening the door to the study of a great variety of transient effects or the couplingwith time-dependent external fields. This methodology |whose computational cost iscomparable to a standard TDDFT calculation| is, to the best of our knowledge, the firstab-initio implementation of this kind reported in the literature. Therefore, the proposedmodel was subjected to a rigorous validation by studying the conductivity of saturatedand unsaturated hydrocarbons and contrasting the results with different formalisms.Fil: Morzan, Uriel Nicolás. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina