A5048997328- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
- Protein Structure and Dynamics
- Machine Learning in Materials Science
- Hemoglobin structure and function
- Covalent Organic Framework Applications
- Combustion and flame dynamics
- Nitric Oxide and Endothelin Effects
- Photochemistry and Electron Transfer Studies
- Electron Spin Resonance Studies
- Metal-Organic Frameworks: Synthesis and Applications
- Crystallography and molecular interactions
- Computational Drug Discovery Methods
- Quantum, superfluid, helium dynamics
- Metal complexes synthesis and properties
- Molecular Spectroscopy and Structure
- Molecular spectroscopy and chirality
- Luminescence and Fluorescent Materials
- Free Radicals and Antioxidants
- Electrocatalysts for Energy Conversion
- Advanced Combustion Engine Technologies
- Enzyme Structure and Function
- Mass Spectrometry Techniques and Applications
- Advanced Physical and Chemical Molecular Interactions
- Electrochemical Analysis and Applications
New York University Abu Dhabi
2024-2025
New York University
2024-2025
University of California, Berkeley
2018-2023
University of Basel
2015-2021
University of South Carolina
2015
We report a new deep learning message passing network that takes inspiration from Newton's equations of motion to learn interatomic potentials and forces.
Quantum chemistry in the form of density functional theory (DFT) calculations is a powerful numerical experiment for predicting intermolecular interaction energies. However, no chemical insight gained this way beyond predictions observables. Energy decomposition analysis (EDA) can quantitatively bridge gap by providing values drivers interactions, such as permanent electrostatics, Pauli repulsion, dispersion, and charge transfer. These energetic contributions are identified performing DFT...
Given the piecewise approach to modeling intermolecular interactions for force fields, they can be difficult parametrize since are fit data like total energies that only indirectly connect their separable functional forms. Furthermore, by neglecting certain types of molecular such as charge penetration and transfer, most classical fields must rely on, but do not always demonstrate, how cancellation errors occurs among remaining accounted exchange repulsion, electrostatics, polarization. In...
Abstract Visual sensing of humidity and temperature by solids plays an important role in the everyday life industrial processes. Due to their hydrophobic nature, most covalent organic framework (COF) sensors often exhibit poor optical response when exposed moisture. To overcome this challenge, is set out improve, moisture incorporating H‐bonding ionic functionalities into COF network. A highly sensitive COF, consisting guanidinium diformylpyridine linkers (TG‐DFP), capable detecting changes...
Cryosurgery represents a transformative approach in the treatment of resistant tumors, utilizing extreme cold to selectively ablate malignant tissue. However, clinical success this technique is constrained by limited ability current imaging techniques differentiate effectively between cancerous and healthy tissues with high spatial resolution. To overcome challenge, we present nanoscale Covalent Organic Framework, nTG-DFP-COF, specifically designed enhance fluorescence-guided cryo-imaging....
In this work, we have developed an anisotropic polarizable model for the AMOEBA force field that is derived from electrostatic fitting on a gas phase water molecule as primary approach to improve many-body polarization model. We validate our using small large cluster benchmark data sets and ambient liquid properties through comparisons variational energy decomposition analysis breakdown of molecular interactions water–ion trimer systems. find accounting anisotropy single demonstrably...
Abstract Nitric oxide binding and unbinding from myoglobin (Mb) is central to the function of protein. By using reactive molecular dynamics (MD) simulations, following NO dissociation were characterized in both time space. Ligand rebinding can be described by two processes on 10 ps 100 timescale, which agrees with recent optical X‐ray absorption experiments. Explicitly including iron out‐of‐plane (Fe‐oop) coordinate essential for a meaningful interpretation data. The proposed existence an...
The generation of reference data for deep learning models is challenging reactive systems, and more so combustion reactions due to the extreme conditions that create radical species alternative spin states during process. Here, we extend intrinsic reaction coordinate (IRC) calculations with ab initio MD simulations normal mode displacement extensively cover potential energy surface 19 channels hydrogen combustion. A total ∼290,000 energies ∼1,270,000 nuclear force vectors are evaluated a...
Nonreactive force fields are defined by perturbations of electron density that relatively small, whereas chemical reactivity involves wholesale electronic rearrangements make and break bonds. Thus, reactive incredibly difficult to develop compared nonreactive fields, yet at the same time, they fill a critical need when ab initio molecular dynamics methods not affordable. We introduce new field model for water combines modified nonbonded terms ReaxFF its embedding in electrostatic...
Aqueous solutions of alkyl/alkaline metal and halide ions play a crucial functional role in biological systems such as proteins, membranes, nucleic acids for interfacial chemistry geomedia the atmosphere. We present MB-UCB many-body force field monovalent divalent that includes polarization, charge penetration to describe short-range permanent electrostatics accurately, well model transfer better quantum mechanical potential energy surface its components obtained from absolutely localized...
Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) reveal physical driving forces behind intermolecular interactions. In EDA, typically interaction from a good-quality density functional theory (DFT) calculation decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli...
We apply two recently developed computational methods, DFTB3 and VALBOND, to study copper oxidation/reduction processes in solution protein. The properties of interest include the coordination structure different oxidation states water or a protein (plastocyanin) active site, reduction potential ion environments, environmental response oxidation. DFTB3/MM VALBOND simulation results are compared DFT/MM simulations experimental whenever possible. For aqueous solution, generally close B3LYP/MM...
The solvent dynamics in Fe-tris-bipyridine [Fe(bpy)3](2+) upon electronic excitation (oxidation) and subsequent relaxation is followed on the picosecond time scale by using atomistic simulations. Starting from low spin (LS) Fe(II)LS state transition to excited Fe(III) (1,3)MLCT (metal-to-ligand charge transfer) decreases water coordination immediate proximity of central iron atom. This readjustment shell occurs subpicosecond scale. Full environment would occur 10 ps which is, however, never...
Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve the description IDPs/IDRs but largely disagreement with solution experiments states. This work considers a new direction-the connection configurational entropy-and how it might change nature our understanding protein field development equally well encompass globular proteins, IDRs/IDPs, disorder-to-order transitions. We have...
The solvent dynamics around fluorinated acetonitrile is characterized by 2-dimensional infrared spectroscopy and atomistic simulations. lineshape of the linear spectrum better captured semiempirical (density functional tight binding) mixed quantum mechanical/molecular mechanics simulations, whereas force field simulations with multipolar interactions yield lineshapes that are significantly too narrow. For dynamics, a relatively slow time scale 2 ps found from experiments supported With...
The conversion of nitric oxide (NO) into nitrate (NO3- ) by dioxygenation protects cells from lethal NO. Starting NO-bound heme, the first step in converting NO benign NO3- is ligand exchange reaction FeNO+O2 →FeO2 +NO, which still poorly understood at a molecular level. For wild-type (WT) truncated hemoglobin N (trHbN) and its Y33A mutant, calculated barriers for differ 1.5 kcal mol-1 , compared with 1.7 experiment. It directly confirmed that rate-limiting trHbN entropic contributions...
To study intermolecular interactions involving radicals at the correlated level, energy decomposition analysis scheme for second-order Mo̷ller-Plesset perturbation theory based on absolutely localized molecular orbitals (ALMO-MP2-EDA) is generalized to unrestricted and restricted open-shell MP2. The benefit of MP2 that it can provide accurate binding energies radical complexes where density functional be error-prone due delocalization errors. As a model application, ALMO-MP2-EDA applied...
Covalent Organic Frameworks Guanidinium and diformylpyridine units are linked to form a covalent organic framework (COF). The hydrophilic COF responds humidity temperature, making it competitive sensor. incorporation of ionic moieties creates hydrogen bonds between the entrapped water framework, which restricts rotation leads reversible thermochromism fluorescent hydrochromism in solid state. More article number 2311064, Ali Trabolsi co-workers.
The implementation, validation, and application of the multi-state VALBOND method for transition-metal-containing hypervalent molecules are presented. This approach is particularly suited with unusual shapes systems that need to be described by a superposition resonance structures, each which satisfies octet rule. implementation based on original force field allows us smoothly switch between can characterized its own field, including varying charge distributions coupling terms states....
The dynamics and spectroscopy of N-methyl-acetamide (NMA) trialanine in solution are characterized from molecular simulations using different energy functions, including a conventional point charge (PC)-based force field, one based on multipolar (MTP) representation the electrostatics, semiempirical DFT method. For 1D infrared spectra, frequency splitting between two amide-I groups is 10 cm–1 PC, 13 MTP, 47 self-consistent density functional tight-binding (SCC-DFTB) simulations, compared...
Structural characterization of the copper-coordination shell is important in catalysis and biology. Cu-containing domains are prevalent biological systems play roles oxidation electron transport process. Here, solution structure, solvent organization, dynamics around aqueous [Cu(II)(Imidazole)4] were characterized using atomistic simulations. Asymmetric axial water coordination metal atom was found which agrees with results from Minuit X-ray absorption near-edge structure (MXAN) experiments....
Developing a low‐cost, robust, and high‐performance electrocatalyst capable of efficiently performing both the oxygen evolution reaction hydrogen (HER) under basic acidic conditions is major challenge. This area research has attracted much attention in recent decades due to its importance energy storage conversion. Herein, we report synthesis two imine‐linked isoindigo‐based covalent organic networks. The combination isoindigo dialdehyde with planar triazine core, leads formation thin,...
Developing a low‐cost, robust, and high‐performance electrocatalyst capable of efficiently performing both the oxygen evolution reaction hydrogen (HER) under basic acidic conditions is major challenge. This area research has attracted much attention in recent decades due to its importance energy storage conversion. Herein, we report synthesis two imine‐linked isoindigo‐based covalent organic networks. The combination isoindigo dialdehyde with planar triazine core, leads formation thin,...