4 research outputs found
Effects of temperature on the shape and symmetry of molecules and solids
Despite its undeniable problems from a philosophical point of view, the concept of molecular structure, with attributes such as shape and symmetry, directly borrowed from the description of macroscopic objects, is nowadays central to most of chemistry. Following this trend, descriptions such as "the tetrahedral" carbon atom are widely used from elementary textbooks to the most up-to-date research articles. The definition of molecular shape is, however, not as simple as it might seem at first sight. Molecules don't behave as macroscopic objects do due to the incessant motion of its constituent particles, nuclei and electrons. How are molecular shape and symmetry affected by this thermal motion? In this review we introduce the language of continuous symmetry measures as a new tool to quantitatively describe the effects of temperature on molecular shape and symmetry
Conformational analysis of enantiomerization coupled to internal rotation in triptycyl-n-helicenes
We present a computational study of a reduced potential energy surface (PES) to describe enantiomerization and internal rotation in three triptycyl-n-helicene molecules, centering the discussion on the issue of a proper reaction coordinate choice. To reflect the full symmetry of both strongly coupled enantiomerization and rotation processes, two non-fixed combinations of dihedral angles must be used, implying serious computational problems that required the development of a complex general algorithm. The characteristic points on each PES are analyzed, the intrinsic reaction coordinates are calculated, and finally they are projected on the reduced PES. Unlike what was previously found for triptycyl-3-helicene, the surfaces for triptycyl-4-helicene and triptycyl-5-helicene contain valley-ridge-inflection (VRI) points. The reaction paths on the reduced surfaces are analyzed to understand the dynamical behaviour of these molecules and to evaluate the possibility of a molecule of this family exhibiting a Brownian ratchet behaviour
Carpeta docent / Bienni 2011-2013 - Abel Carreras Conill
MĂ ster de Docència UniversitĂ ria per a Professorat Novell, Institut de Ciències de l'EducaciĂł, Universitat de Barcelona. Bienni: 2011-2013. Mentor: Miquel Llunell i MarĂ.Es presenta la carpeta docent elaborada en el context del mĂ ster i l'aplicaciĂł a l'assignatura de "Recursos informĂ tics" de la Facultat de QuĂmica de la Universitat de Barcelona
Estudi teòric de l’estereodinà mica de rotors i engranatges moleculars
[cat] Els rotors, motors i engranatges moleculars sĂłn molècules o sistemes moleculars que tenen com a caracterĂstica que presenten moviments conformacionals de gran amplitud, majoritĂ riament associats a rotacions internes al voltant d’un o diversos enllaços senzills entre els seus Ă toms. Aquesta propietat permet a aquestes molècules adoptar diferents geometries conformacionals en funciĂł de la rotaciĂł al voltant d’aquests enllaços, podent donar comportaments mecĂ nics anĂ logs al dĘĽengranatges macroscòpics, de manera que aquestes molècules puguin ser considerades com a components bĂ sics per a un futur disseny de mĂ quines nanoscòpiques mĂ©s complexes. És per aquesta raĂł que l'anĂ lisi del comportament dinĂ mic de rotors i engranatges moleculars ha despertat l’interès d’una gran quantitat de cientĂfics que, des de fa temps, treballen en la sĂntesi i caracteritzaciĂł d’aquest tipus de compostos. Una manera de poder abordar l’estudi teòric dels rotors moleculars sense haver de renunciar a l’ús d’un mètode de cĂ lcul de les interaccions intermoleculars acurat, Ă©s efectuant una dinĂ mica molecular restringida, on nomĂ©s es tenen en compte un nombre reduĂŻt de graus de llibertat mentre que els efectes de la resta modes en el comportament dinĂ mic es menysprea o s’inclou nomĂ©s de manera aproximada com a pertorbaciĂł del moviment que s’estudia en detall. D’aquesta manera Ă©s possible reduir el cost computacional del cĂ lcul i poder accedir aixĂ, a temps de simulaciĂł molt mĂ©s elevats amb un cost computacional assumible. En aquesta tesi doctoral s’ha desenvolupat un conjunt de programes informĂ tics que permeten simular el comportament dinĂ mic de sistemes formats per un nombre de fragments que es consideren rĂgids amb una energia potencial total definida a partir d’interaccions a parells entre ells. Això permet tractar sistemes grans reduint el nombre de graus de llibertat, separant aixĂ les interaccions mĂ©s rellevants. D’aquesta manera, al tenir en compte nomĂ©s uns pocs graus de llibertat, es pot realitzar un cĂ lcul mĂ©s precĂs de l’energia en un temps assumible. Per tal de descriure les interaccions entre fragments s’han calculat superfĂcies de potencial en funciĂł de les variables que descriuen les rotacions internes entre fragments rĂgids. Aquesta descripciĂł, permet veure mĂ©s clarament els possibles acoblaments entre els diferents graus de llibertat rotacionals de la molècula. Per fer-ho, s’ha elaborat una metodologia que permet descriure els processos de flexiĂł que tenen lloc a la molècula al mateix temps que Ă©s produeix la rotaciĂł. Amb aquesta metodologia, s’ha realitzat l’estudi dels tripticil[n]helicens, molècules formades per la uniĂł d’un grup tripticil i un helicè mitjançant un enllaç senzill, que han estat estudiades per la seva relaciĂł amb els anomenats trinquets moleculars, sistemes on hi ha una rotaciĂł interna en un entorn asimètric degut a la presència de fragments moleculars quirals. Utilitzant programes de simulaciĂł de Monte Carlo i de dinĂ mica molecular desenvolupats en el transcurs de la tesi s’ha estudiat tambĂ© en col•laboraciĂł amb el grup experimental del Prof. Miguel A. Garcia-Garibay de la Universitat de California, dos cristalls amfidinĂ mics, sòlids on fragments de les molècules empaquetades conserven una alta llibertat de rotaciĂł, sintetitzats recentment: el rotor de mestranol i l’IDipp-C60.[eng] Molecular motors, rotors and gears are complex molecules that undergo wide conformational movements that mimic those of their macroscopic mechanical counterparts. For this reason these molecular systems have recently been the subject of numerous experimental and theoretical studies with the aim to incorporate them as basic building blocks of more complex nanoscopic devices. Due to their intrinsic structural complexity it is difficult to perform accurate dynamical studies using standard molecular dynamics techniques considering all atoms of the system and for this reason in this thesis we have developed programs to simulate the dynamical behavior of such systems !considering only a restricted set of degrees of freedom. The systems are modeled by a collection of rigid fragments that interact through pair potentials that lead to a reduced potential energy surface for the relevant degrees of freedom that is being used in conjunction of molecular dynamics or Monte Carlo simulation techniques to study the dynamic behavior of molecular gears or ensembles of molecular rotors. Using the general purpose molecular dynamics and Monte Carlo programs developed in this thesis have also been adapted to be used in the study of the dynamical behavior of amphidynamic solids, a new class of molecular crystals where some fragments of the constituent molecules exhibit large conformational motions. This part of the work, devoted to the simulation of the dynamic behavior of the mestranol rotor and the crystals of IDipp-C60 has been developed in collaboration with the experimental group of Prof. Miguel Angel GarcĂa Garibay at UCLA that worked in the synthesis and experimental characterization of these two compounds