Search results for "Ab initio molecular dynamics"

Reply to Comment on “Mixed Grotthuss and Vehicle Transport Mechanism in Proton Conducting Polymers from Ab initio Molecular Dynamics Simulations”

2011

Magic triangular and tetrahedral clusters

1997

Using the methods of density functional theory and the jellium model we show that clusters with triangular [in two dimensions (2D)] or tetrahedral [in three dimensions (3D)] shapes have a strong shell structure and enhanced stability. Moreover, the shell closings correspond to the lowest magic numbers of a 2D and 3D harmonic oscillator and at the same time to the number of divalent atoms in close-packed triangles and tetrahedrons. Ab initio molecular dynamics simulations for Na and Mg clusters support the results of the jellium model.

Revisiting the Nonadiabatic Process in 1,2-Dioxetane.

2015

Determining the ground and excited-state decomposition mechanisms of 1,2-dioxetane is essential to understand the chemiluminescence and bioluminescence phenomena. Several experimental and theoretical studies has been performed in the past without reaching a converged description. The reason is in part associated with the complex nonadiabatic process taking place along the reaction. The present study is an extension of a previous work (De Vico, L.; Liu, Y.-J.; Krogh, J. W.; Lindh, R. J. Phys. Chem. A 2007, 111, 8013-8019) in which a two-step mechanism was established for the chemiluminescence involving asynchronous O-O' and C-C' bond dissociations. New high-level multistate multi configurati…

Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution

2015

Ab initio molecular dynamics (AIMD) simulations in trimethylamine N-oxide (TMAO)-D2O solution are employed to elucidate the effects of TMAO on the reorientational dynamics of D2O molecules. By decomposing the O-D groups of the D2O molecules into specific subensembles, we reveal that water reorientational dynamics are retarded considerably in the vicinity of the hydrophilic TMAO oxygen (O(TMAO)) atom, due to the O-D···O(TMAO) hydrogen-bond. We find that this reorientational motion is governed by two distinct mechanisms: The O-D group rotates (1) after breaking the O-D···O(TMAO) hydrogen-bond, or (2) together with the TMAO molecule while keeping this hydrogen-bond intact. While the orientatio…

Short hydrogen bonds enhance nonaromatic protein-related fluorescence

2021

Significance Intrinsic fluorescence of nonaromatic amino acids is a puzzling phenomenon with an enormous potential in biophotonic applications. The physical origins of this effect, however, remain elusive. Herein, we demonstrate how specific hydrogen bond networks can modulate fluorescence. We highlight the key role played by short hydrogen bonds, present in the protein structure, on the ensuing fluorescence. We provide detailed experimental and molecular evidence to explain these unusual nonaromatic optical properties. Our findings should benefit the design of novel optically active biomaterials for applications in biosensing and imaging.

First principles simulation of amorphous InSb

2013

Ab initio molecular dynamics simulations based on density functional theory have been performed to generate a model of amorphous InSb by quenching from the melt. The resulting network is mostly tetrahedral with a minor fraction ($10%$) of atoms in a fivefold coordination. The structural properties are in good agreement with available x-ray diffraction and extended x-ray-absorption fine structure data and confirm the proposed presence of a sizable fraction of homopolar In-In and Sb-Sb bonds whose concentration in our model amounts to about $20%$ of the total number of bonds.

Ab initio molecular dynamics study of overtone excitations in formic acid and its water complex

2018

In this article, we present results from ab initio molecular dynamics simulation of overtone excitation in formic acid monomer and its water complex in the gas phase. For the monomer, a conformation change is observed employing both OH and CH vibrational excitations, which supports experimental findings. In the formic acid–water complex, interconversion also takes place, but it proceeds via hydrogen exchange rather than via intramolecular reaction. Simulations raise a question on effect of quantum and matrix effects to the results. Also, a brief test of different computation methods was done on the system. peerReviewed

Vibrational Signature of Water Molecules in Asymmetric Hydrogen Bonding Environments

2013

The O–H stretching vibrational modes of water molecules are sensitive to their local environments. Here, we applied effective normal-mode analysis to isolate contributions of each of the two hydrogen atoms to the vibrational modes ν1 and ν3 of water molecules in the liquid phase. We demonstrate that the decoupling of the two contributions fd and the frequency splitting of the vibrational modes Δω13 are inextricably related to the symmetry of the hydrogen bonding environment. We show that ambient liquid water modeled at the density functional level of theory exhibits the characteristics of an asymmetric environment with an average decoupling of 0.82 and a splitting of 137 inverse centimeters…

Electronic-structure-induced deformations of liquid metal clusters

1995

Ab initio molecular dynamics is used to study deformations of sodium clusters at temperatures $500\cdots 1100$ K. Open-shell Na$_{14}$ cluster has two shape isomers, prolate and oblate, in the liquid state. The deformation is stabilized by opening a gap at the Fermi level. The closed-shell Na$_8$ remains magic also at the liquid state.

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies

2013

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 cluste…