Calicheamicin-DNA complexes: warhead alignment and saccharide recognition of the minor groove.

The solution structures of calicheamicin gamma 1I, its cycloaromatized analog (calicheamicin epsilon), and its aryl tetrasaccharide complexed to a common DNA hairpin duplex have been determined by NMR and distance-refined molecular dynamics computations. Sequence specificity is associated with carbohydrate-DNA recognition that places the aryl tetrasaccharide component of all three ligands in similar orientations in the minor groove at the d(T-C-C-T).d(A-G-G-A) segment. The complementary fit of the ligands and the DNA minor groove binding site creates numerous van der Waals contacts as well as hydrogen bonding interactions. Notable are the iodine and sulfur atoms of calicheamicin that hydrogen bond with the exposed amino proton of the 5'- and 3'-guanines, respectively, of the d(A-G-G-A) segment. The sequence-specific carbohydrate binding orients the enediyne aglycone of calicheamicin gamma 1I such that its C3 and C6 proradical centers are adjacent to the cleavage sites. While the enediyne aglycone of calicheamicin gamma 1I is tilted relative to the helix axis and spans the minor groove, the cycloaromatized aglycone is aligned approximately parallel to the helix axis in the respective complexes. Specific localized conformational perturbations in the DNA have been identified from imino proton complexation shifts and changes in specific sugar pucker patterns on complex formation. The helical parameters for the carbohydrate binding site are comparable with corresponding values in B-DNA fibers while a widening of the groove is observed at the adjacent aglycone binding site.

Simulação e modelagem computacional de dados de espalhamento à baixos ângulos - enfoque em estruturas de alta simetria

Esta tese apresenta uma abordagem para a criação rápida de modelos em diferentes geometrias (complexas ou de alta simetria) com objetivo de calcular a correspondente intensidade espalhada, podendo esta ser utilizada na descrição de experimentos de es- palhamento à baixos ângulos. A modelagem pode ser realizada com mais de 100 geome- trias catalogadas em um Banco de Dados, além da possibilidade de construir estruturas a partir de posições aleatórias distribuídas na superfície de uma esfera. Em todos os casos os modelos são gerados por meio do método de elementos finitos compondo uma única geometria, ou ainda, compondo diferentes geometrias, combinadas entre si a partir de um número baixo de parâmetros. Para realizar essa tarefa foi desenvolvido um programa em Fortran, chamado de Polygen, que permite modelar geometrias convexas em diferentes formas, como sólidos, cascas, ou ainda com esferas ou estruturas do tipo DNA nas arestas, além de usar esses modelos para simular a curva de intensidade espalhada para sistemas orientados e aleatoriamente orientados. A curva de intensidade de espalhamento é calculada por meio da equação de Debye e os parâmetros que compõe cada um dos modelos, podem ser otimizados pelo ajuste contra dados experimentais, por meio de métodos de minimização baseados em simulated annealing, Levenberg-Marquardt e algorítmicos genéticos. A minimização permite ajustar os parâmetros do modelo (ou composição de modelos) como tamanho, densidade eletrônica, raio das subunidades, entre outros, contribuindo para fornecer uma nova ferramenta para modelagem e análise de dados de espalhamento. Em outra etapa desta tese, é apresentado o design de modelos atomísticos e a sua respectiva simulação por Dinâmica Molecular. A geometria de dois sistemas auto-organizado de DNA na forma de octaedro truncado, um com linkers de 7 Adeninas e outro com linkers de ATATATA, foram escolhidas para realizar a modelagem atomística e a simulação por Dinâmica Molecular. Para este sistema são apresentados os resultados de Root Mean Square Deviations (RMSD), Root Mean Square Fluctuations (RMSF), raio de giro, torção das hélices duplas de DNA além da avaliação das ligações de Hidrogênio, todos obtidos por meio da análise de uma trajetória de 50 ns.

Efeito do macrodipolo sobre a estabilidade térmica de derivados de 1,3,5-tricarboxamida-ciclo-hexano

1,3,5-tricarboxamida-ciclo-hexano são compostos capazes de se autoagregarem formando colunas supramoleculares as quais se mantêm unidas não só devido às interações das cadeias laterais mas também devido às ligações de hidrogênio de cada um dos três grupos amida por monômero. Cada monômero possui momento de dipolo elétrico associado aos grupos amida. Quando as amidas dos vários monômeros dentro da mesma coluna estão apontadas para a mesma direção, os momentos de dipolo individuais de todas as amidas se somam formando elevado dipolo ao longo do eixo da coluna, chamado de macrodipolo, o qual influencia as interações intercolunares. Neste trabalho foram investigadas quatro conformações as quais diferem entre si em relação à orientação dos grupos carbonila: a conformação Up-Up contém grupos carbonilas paralelos dentro das colunas e colunas paralela, a conformação Up-Down possui grupos carbonilas paralelos dentro das colunas e colunas antiparalelas, a conformação Intra-Up-Up contém grupos carbonilas antiparalelos dentro das colunas e colunas paralelas e a conformação Intra-Up-Down possui grupos carbonilas antiparalelos dentro das colunas e colunas antiparalelas. Foi usado Dinâmica Molecular Clássica para investigar o efeito das interações macrodipolo-macrodipolo das quatro diferentes conformações sobre a estabilidade térmica de três diferentes compostos derivados de 1,3,5-tricarboxamida-ciclo-hexano. Foi verificado que as conformações com colunas antiparalelas tendem a ser ligeiramente mais estáveis do que as conformações com orientação paralela. O efeito da orientação dos grupos carbonila dentro das colunas sob a estabilidade do material está relacionado a vários fatores, tais como cargas atômicas parciais, arranjo colunar ou natureza das cadeias laterais, e os resultados não são tão diretos como quando se compara as orientações entre colunas. Outro tópico investigado foi o comportamento do material durante a transição da fase colunar para a fase desordenada. As colunas podem se desmontar em três diferentes formas: elas podem completamente se desintegrar rapidamente, podem primeiro se desintegrar lentamente e então perder a ordem colunar ou primeiro perdem a ordem colunar e então se desmontam em um processo demorado. Tais comportamentos estão associados com as interações dentro e entre colunas.

Formation of a metallic contact: jump to contact revisited

The transition from tunneling to metallic contact between two surfaces does not always involve a jump, but can be smooth. We have observed that the configuration and material composition of the electrodes before contact largely determine the presence or absence of a jump. Moreover, when jumps are found preferential values of conductance have been identified. Through a combination of experiments, molecular dynamics, and first-principles transport calculations these conductance values are identified with atomic contacts of either monomers, dimers, or double-bond contacts.

Mechanical annealing of metallic electrodes at the atomic scale

The process of creating an atomically defined and robust metallic tip is described and quantified using measurements of contact conductance between gold electrodes and numerical simulations. Our experiments show how the same conductance behavior can be obtained for hundreds of cycles of formation and rupture of the nanocontact by limiting the indentation depth between the two electrodes up to a conductance value of approximately 5G0 in the case of gold. This phenomenon is rationalized using molecular dynamics simulations together with density functional theory transport calculations which show how, after repeated indentations (mechanical annealing), the two metallic electrodes are shaped into tips of reproducible structure. These results provide a crucial insight into fundamental aspects relevant to nanotribology or scanning probe microscopies.

Mechanical, electrical, and magnetic properties of Ni nanocontacts

The dynamic deformation upon stretching of Ni nanowires as those formed with mechanically controllable break junctions or with a scanning tunneling microscope is studied both experimentally and theoretically. Molecular dynamics simulations of the breaking process are performed. In addition, and in order to compare with experiments, we also compute the transport properties in the last stages before failure using the first-principles implementation of Landauer's formalism included in our transport package ALACANT.

Understanding the structure of the first atomic contact in gold

We have studied experimentally jump-to-contact (JC) and jump-out-of-contact (JOC) phenomena in gold electrodes. JC can be observed at first contact when two metals approach each other, while JOC occurs in the last contact before breaking. When the indentation depth between the electrodes is limited to a certain value of conductance, a highly reproducible behaviour in the evolution of the conductance can be obtained for hundreds of cycles of formation and rupture. Molecular dynamics simulations of this process show how the two metallic electrodes are shaped into tips of a well-defined crystallographic structure formed through a mechanical annealing mechanism. We report a detailed analysis of the atomic configurations obtained before contact and rupture of these stable structures and obtained their conductance using first-principles quantum transport calculations. These results help us understand the values of conductance obtained experimentally in the JC and JOC phenomena and improve our understanding of atomic-sized contacts and the evolution of their structural characteristics.

Dynamic bonding of metallic nanocontacts: Insights from experiments and atomistic simulations

The conductance across an atomically narrow metallic contact can be measured by using scanning tunneling microscopy. In certain situations, a jump in the conductance is observed right at the point of contact between the tip and the surface, which is known as “jump to contact” (JC). Such behavior provides a way to explore, at a fundamental level, how bonding between metallic atoms occurs dynamically. This phenomenon depends not only on the type of metal but also on the geometry of the two electrodes. For example, while some authors always find JC when approaching two atomically sharp tips of Cu, others find that a smooth transition occurs when approaching a Cu tip to an adatom on a flat surface of Cu. In an attempt to show that all these results are consistent, we make use of atomistic simulations; in particular, classical molecular dynamics together with density functional theory transport calculations to explore a number of possible scenarios. Simulations are performed for two different materials: Cu and Au in a [100] crystal orientation and at a temperature of 4.2 K. These simulations allow us to study the contribution of short- and long-range interactions to the process of bonding between metallic atoms, as well as to compare directly with experimental measurements of conductance, giving a plausible explanation for the different experimental observations. Moreover, we show a correlation between the cohesive energy of the metal, its Young's modulus, and the frequency of occurrence of a jump to contact.

Dynamical Equations For The Period Vectors In A Periodic System Under Constant External Stress

The purpose of this paper is to derive the dynamical equations for the period vectors of a periodic system under constant external stress. The explicit starting point is Newton’s second law applied to halves of the system. Later statistics over indistinguishable translated states and forces associated with transport of momentum are applied to the resulting dynamical equations. In the final expressions, the period vectors are driven by the imbalance between internal and external stresses. The internal stress is shown to have both full interaction and kinetic-energy terms.

Mécanismes de transfert de proton d’une réaction acido-basique en phase aqueuse : une étude ab-initio

Les réactions de transfert de proton se retrouvent abondamment dans la nature et sont des processus cruciaux dans plusieurs réactions chimiques et biologiques, qui se produisent souvent en milieu aqueux. Les mécanismes régissant ces échanges de protons sont complexes et encore mal compris, suscitant un intérêt des chercheurs en vue d’une meilleure compréhension fondamentale du processus de transfert. Le présent manuscrit présente une étude mécanistique portant sur une réaction de transfert de proton entre un acide (phénol fonctionnalisé) et une base (ion carboxylate) en phase aqueuse. Les résultats obtenus sont basés sur un grand nombre de simulations de dynamique moléculaire ab-initio réalisées pour des systèmes de type « donneur-pont-accepteur », où le pont se trouve à être une unique molécule d’eau, permettant ainsi l’élaboration d’un modèle cinétique détaillé pour le système étudié. La voie de transfert principalement observée est un processus ultra-rapide (moins d’une picoseconde) passant par la formation d’une structure de type « Eigen » (H9O4+) pour la molécule d’eau pontante, menant directement à la formation des produits. Une seconde structure de la molécule d’eau pontante est également observée, soit une configuration de type « Zündel » (H5O2+) impliquant l’accepteur de proton (l’ion carboxylate) qui semble agir comme un cul-de-sac pour la réaction de transfert de proton.

Mécanismes de transfert de proton d’une réaction acido-basique en phase aqueuse : une étude ab-initio

Les réactions de transfert de proton se retrouvent abondamment dans la nature et sont des processus cruciaux dans plusieurs réactions chimiques et biologiques, qui se produisent souvent en milieu aqueux. Les mécanismes régissant ces échanges de protons sont complexes et encore mal compris, suscitant un intérêt des chercheurs en vue d’une meilleure compréhension fondamentale du processus de transfert. Le présent manuscrit présente une étude mécanistique portant sur une réaction de transfert de proton entre un acide (phénol fonctionnalisé) et une base (ion carboxylate) en phase aqueuse. Les résultats obtenus sont basés sur un grand nombre de simulations de dynamique moléculaire ab-initio réalisées pour des systèmes de type « donneur-pont-accepteur », où le pont se trouve à être une unique molécule d’eau, permettant ainsi l’élaboration d’un modèle cinétique détaillé pour le système étudié. La voie de transfert principalement observée est un processus ultra-rapide (moins d’une picoseconde) passant par la formation d’une structure de type « Eigen » (H9O4+) pour la molécule d’eau pontante, menant directement à la formation des produits. Une seconde structure de la molécule d’eau pontante est également observée, soit une configuration de type « Zündel » (H5O2+) impliquant l’accepteur de proton (l’ion carboxylate) qui semble agir comme un cul-de-sac pour la réaction de transfert de proton.

Data index for energy transfer collisions of atoms and molecules, 1970-1979 /

Mode of access: Internet.

Zur molecularphysik,

Mode of access: Internet.

Function and Regulation of Cytochrome P450 4V2 and the Implications in Bietti’s Crystalline Dystrophy

Thesis (Ph.D.)--University of Washington, 2016-06

High-pressure adsorption of supercritical gases on activated carbons: An improved approach based on the density functional theory and the bender equation of state

Adsorption of nitrogen, argon, methane, and carbon dioxide on activated carbon Norit R1 over a wide range of pressure (up to 50 MPa) at temperatures from 298 to 343 K (supercritical conditions) is analyzed by means of the density functional theory modified by incorporating the Bender equation of state, which describes the bulk phase properties with very high accuracy. It has allowed us to precisely describe the experimental data of carbon dioxide adsorption slightly above and below its critical temperatures. The pore size distribution (PSD) obtained with supercritical gases at ambient temperatures compares reasonably well with the PSD obtained with subcritical nitrogen at 77 K. Our approach does not require the skeletal density of activated carbon from helium adsorption measurements to calculate excess adsorption. Instead, this density is treated as a fitting parameter, and in all cases its values are found to fall into a very narrow range close to 2000 kg/m(3). It was shown that in the case of high-pressure adsorption of supercritical gases the PSD could be reliably obtained for the range of pore width between 0.6 and 3 run. All wider pores can be reliably characterized only in terms of surface area as their corresponding excess local isotherms are the same over a practical range of pressure.