اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدAn ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
248
0
0.0
(
0
)
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
قيم البحث
اقرأ أيضاً
We describe a simplified approach to simulating Raman spectra using ab initio molecular dynamics (AIMD) calculations. Our protocol relies on on-the-fly calculations of approximate molecular polarizabilities using a sum over orbitals (as opposed to states) method.
We perform on-the-fly non-adiabatic molecular dynamics simulations using the symmetrical quasi-classical (SQC) approach with the recently suggested molecular Tully models: ethylene and fulvene. We attempt to provide benchmarks of the SQC methods usin
g both the square and the triangle windowing schemes as well as the recently proposed electronic zero-point-energy correction scheme (so-called the gamma correction). We use the quasi-diabatic propagation scheme to directly interface the diabatic SQC methods with adiabatic electronic structure calculations. Our results showcase the drastic improvement of the accuracy by using the trajectory-adjusted gamma-corrections, which outperform the widely used trajectory surface hopping method with decoherence corrections. These calculations provide useful and non-trivial tests to systematically investigate the numerical performance of various diabatic quantum dynamics approaches, going beyond simple diabatic model systems that have been used as the major workhorse in the quantum dynamics field. At the same time, these available benchmark studies will also likely foster the development of new quantum dynamics approaches based on these techniques.
Ab initio molecular dynamics (AIMD) is a valuable technique for studying molecules and materials at finite temperatures where the nuclei evolve on potential energy surfaces obtained from accurate electronic structure calculations. In this work, a qua
ntum computer-based AIMD method is presented. The electronic energies are calculated on a quantum computer using the variational quantum eigensolver (VQE) method. We compute the energy gradients numerically using the Hellmann-Feynman theorem, finite differences, and a correlated sampling technique. Our method only requires additional classical calculations of electron integrals for each degree of freedom, without any additional computations on a quantum computer beyond the initial VQE run. To achieve comparable accuracy, our gradient calculation method requires three to five orders of magnitude fewer measurements than other brute force methods without correlated sampling. As a proof of concept, AIMD dynamics simulations are demonstrated for the H2 molecule on IBM quantum devices. To the best of our knowledge, it is the first successful attempt to run AIMD on quantum devices for a chemical system. In addition, we demonstrate the validity of the method for larger molecules using full configuration interaction (FCI) wave functions. As quantum hardware and noise mitigation techniques continue to improve, the method can be utilized for studying larger molecular and material systems.
Ultrafast dynamics in chemical systems provide a unique access to fundamental processes at the molecular scale. A proper description of such systems is often very challenging because of the quantum nature of the problem. The concept of matrix product
states (MPS), however, has proven its performance in describing such correlated quantum system in recent years for a wide range of applications. In this work, we continue the development of the MPS approach to study ultrafast electron dynamics in quantum chemical systems. The method combines time evolution schemes, such as fourth-order Runge-Kutta and Krylov space time evolution, with MPS, in order to solve the time-dependent Schrodinger equation efficiently. This allows for describing electron dynamics in molecules on a full configurational interaction (CI) level for a few femtoseconds after excitation. As a benchmark, we compare MPS based calculations to full CI calculations for a chain of hydrogen atoms and for the water molecule. Krylov space time evolution is in particular suited for the MPS approach, as it provides a wide range of opportunities to be adjusted to the reduced MPS dimension case. Finally, we apply the MPS approach to describe charge migration effects in iodoacetylene and find direct agreement between our results and experimental observations.
In serine proteases (SPs), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab ini
tio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
