last week in chemistry

43

new preprints about chemistry in the last week

chemRxiv

most active server in chemistry in the last week

coupled cluster

4 preprints

How to Stay out of Trouble in RIXS Calculations Within the Equation-of-Motion Coupled-Cluster Damped Response Theory Framework? Safe Hitchhiking in the Excitation Manifold by Means of Core-Valence Separation

We present a novel approach for computing resonant inelastic X-ray scattering (RIXS) cross sections within the equation-of-motion coupled-cluster (EOM-CC) framework.
5 days ago
chemRxiv

Relativistic many body theory of the electric dipole moment of $^{129}$Xe and its implications for probing new physics beyond the Standard Model

We report the results of our theoretical studies of the time-reversal and parity violating electric dipole moment (EDM) of $^{129}$Xe arising from the nuclear Schiff moment (NSM) and the electron-nucleus tensor-pseudotensor (T-PT) interaction based on the self-consistent and the normal relativistic coupled-cluster methods.
7 days ago
arXiv

Dyson Orbitals within the fc-CVS-EOM-CCSD Framework

We report on the implementation and illustrative applications of Dyson orbitals within the recently proposed frozen-core (fc) core-valence separated (CVS) equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method, which enables efficient and accurate characterization of core-ionized states.
4 days ago
chemRxiv

important role

4 preprints

The Alkaliphilic side of Staphylococcus aureus

In this study, we report physiological roles and catalytic properties of NhaC (NhaC1, NhaC2, and NhaC3), CPA1 (CPA1-1 and CPA1-2) and CPA2 family antiporters and how these antiporters crosstalk with Mnh1, a CPA3 family antiporter, recently shown to play important roles in virulence and pH tolerance.
5 days ago
bioRxiv

Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.
5 days ago
bioRxiv

Basic Mechanism of Sweating and Its Role in Temperature and Appetite Regulation: An Ayurvedic Perspective

They are taking an important role before the action of blood and sweating.
1 day ago
Preprints.org

active site

3 preprints

Uncovering the Role of Key Active Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalysed by Wild-Type and Variants of Triosephosphate Isomerase

Manuscript and supporting information outlining an analysis of an extended Brønsted relationship obtained from empirical valence bond simulations of substrate deprotonation catalyzed by wild-type and mutant variants of triosephosphate isomerase.
6 days ago
chemRxiv

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse and widespread in the environment.

This includes three active site variants inferred to have arisen from the ancestral B3 enzyme.
3 days ago
bioRxiv

Structural control of regioselectivity in an unusual bacterial acyl-CoA dehydrogenase

Furthermore, this regioselectivity is controlled by a combination of bulky residues in the active site and a lateral shift in the positioning of the FAD cofactor within the enzyme.
4 days ago
bioRxiv

ray photoelectron

3 preprints

Selective Growth of Al2O3 on Size-Selected Platinum Clusters by Atomic Layer Deposition

The samples were probed in situ using X-ray photoelectron spectroscopy (XPS), low-energy ion scattering spectroscopy (ISS), and CO temperature-programmed desorption (TPD).
4 days ago
chemRxiv

Dyson Orbitals within the fc-CVS-EOM-CCSD Framework

Here we discuss the simulations of X-ray photoelectron spectra (XPS) and propose an approach to simulate time-resolved (TR-)XPS for probing excited states.
4 days ago
chemRxiv

A novel approach for deducing the mass composition of cosmic rays from lateral densities of EAS particles

A Monte Carlo (MC) simulation study of cosmic ray (CR) extensive air showers (EAS) has been carried out in the energy regime of the KASCADE experiment.
7 days ago
arXiv

experimental data

3 preprints

End-to-End Machine Learning for Experimental Physics: Using Simulated Data to Train a Neural Network for Object Detection in Video Microscopy

Here we demonstrate a `full-stack' computational solution, where the training data set is generated on-the-fly using a noise injection process to produce simulated data characteristic of the experimental system.
7 days ago
arXiv

Flow correlation as a measure of phase transition: results from a new hydrodynamic code

Finding the existence and the location of the QCD critical point on the temperature T and baryon chemical potential $\mu_{b}$ plane is one of the main goals of the RHIC beam energy scan program.
5 days ago
arXiv

A modified Coulomb's law for the tangential debonding of osseointegrated implants

Overall, the results show close agreement with the experimental data, especially the peak and the softening part of the torque curve with a relative error of less than 2.25 %.
7 days ago
arXiv

molecular dynamics

3 preprints

Giant temperature dependence of the Mott gap size in 1T-TaS$_2$ : a molecular dynamics study

The lattice thermodynamics of 1T-TaS$_2$, e.g. the spontaneous formation of periodic distortion and vibrations around the equilibrium position, is calculated by ab initio molecular dynamics.
7 days ago
arXiv

Structure and dynamics of a lipid nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations

We reconcile these views by using a Bayesian/Maximum Entropy method to combine molecular dynamics simulations of MSP1D1{Delta}H5 with the NMR and SAXS experiments.
7 days ago
bioRxiv

Investigating dual Ca2+ modulation of the ryanodine receptor 1 by molecular dynamics simulation

Toward elucidating the Ca2+-modulation mechanism of RyR1, we performed extensive molecular dynamics simulation of the core RyR1 structure in the presence and absence of bound and solvent Ca2+ (total simulation time is 5 microseconds).
3 days ago
bioRxiv

proton transfer

3 preprints

Observations and Theories of Quantum Effects in Proton Transfer Electrode Processes

In this review, we summarize the experimental/theoretical concept of electrochemical quantum proton tunneling (EQPT), which is a key element in microscopic electrode processes.
3 days ago
chemRxiv

Towards Sustainable Synthesis of Polyesters: A QM/MM Study of the Enzymes CalB and AfEST

We found that bond forming/breaking events are concerted with proton transfer to or from the catalytic histidine in all the transition states, but with different degrees of coupling between the motions of the atoms involved.
3 days ago
chemRxiv

mechanics molecular

2 preprints

Towards Sustainable Synthesis of Polyesters: A QM/MM Study of the Enzymes CalB and AfEST

Here we compare in detail the catalytic mechanisms for polycaprolactone synthesis by the enzymes Archaeoglobus fulgidus carboxylesterase (AfEST) and Candida antarctica lipase B (CalB) by performing Quantum mechanics calculations and Quantum Mechanics/Molecular Mechanics Molecular Dynamics simulations.
3 days ago
chemRxiv

core valence

2 preprints

How to Stay out of Trouble in RIXS Calculations Within the Equation-of-Motion Coupled-Cluster Damped Response Theory Framework? Safe Hitchhiking in the Excitation Manifold by Means of Core-Valence Separation

We demonstrate that this problematic behavior can be avoided by extending the core-valence separation (CVS) scheme, which decouples the valence-occupied and core-occupied excitation manifolds, into the response domain.
5 days ago
chemRxiv

Dyson Orbitals within the fc-CVS-EOM-CCSD Framework

We report on the implementation and illustrative applications of Dyson orbitals within the recently proposed frozen-core (fc) core-valence separated (CVS) equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method, which enables efficient and accurate characterization of core-ionized states.
4 days ago
chemRxiv

Boosting the Bounds of Symbolic QED for Effective Pre-Silicon Verification of Processor Cores

Using open-source RISC-V cores, we demonstrate the following: 1.
2 days ago
engrXiv

metal organic

2 preprints

Orthogonal Synthesis of Highly Porous Zr-MOFs Assembled from Simple Building Blocks for Oxygen Storage

The last decade has witnessed significant advances in the scale-up synthesis of metal–organic frameworks (MOFs) using commercially available and affordable organic linkers.
6 days ago
chemRxiv

molecular recognition

2 preprints

Predicting Macrocyclic Molecular Recognition with Machine Learning

DFT, NMR, ITC, and cell confluence data are used to generate predictive algorithms of supramolecular binding to cucurbit[7]uril and experimentally validate these predictions.
6 days ago
chemRxiv

Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters

A stochastic model confirms the presence of an autocatalytic network driven by molecular recognition, where the larger clusters are the only products stabilised by information contained in the cycle, isolated due to a critical transition in the network.
5 days ago
chemRxiv

schiff base

2 preprints

Tetranuclear Copper and Mononuclear Nickel Complex of the Schiff Base of (3Z)-3-Hydrazonobutan-2-One Oxime with Different Aromatic Carbonyl Compounds: Synthesis, Single Crystal X-Ray Structure, Catecholase Activity, Phenoxazinone Synthase Activity, Catalytic Study for the Homocoupling of Benzyl Amines

Synthesis and characterisation of one trinuclear copper complex, ([Cu3L3O]ClO4) (1) and one nickel complex ([Ni(L'H)2(dmso)2](ClO4)2) (2) with Schiff base ligands: (3Z)-3-((Z)-(1-(thiophen-2-yl)ethylidene)hydrazono)butan-2-one oxime (LH) and 1-(pyridin-2-yl)ethylidene)hydrazono)butan-2-one oxime (L'H). 1 shows high...
3 days ago
chemRxiv

Air-Stable Hexagonal Bipyramidal Dysprosium(III) Single-Ion Magnets with Nearly Perfect D6h Local Symmetry

Here we show by using the hexaaza macrocyclic Schiff base ligand and fine-tuning the axial alkoxide/phenol type ligands, a family of hexagonal-bipyramidal Dy(III) complexes, namely [DyIII(L)(Cl)2(H2O/CH3OH)]Cl 1, [DyIII(L)(C6F5O)2(H2O)](BPh4)·2, [DyIII(L)(PhO)2](BPh4) 3, [DyIII(L)(4-MeO-PhO)2](BPh4) 4, [DyIII(L)(naPhO)2](BPh4)...
5 days ago
chemRxiv

equation of motion

2 preprints

How to Stay out of Trouble in RIXS Calculations Within the Equation-of-Motion Coupled-Cluster Damped Response Theory Framework? Safe Hitchhiking in the Excitation Manifold by Means of Core-Valence Separation

However, the convergence of response equations in the X-ray frequency range is often erratic due to the resonant nature of the virtual core-excited states embedded in the valence ionization continuum.
5 days ago
chemRxiv

Dyson Orbitals within the fc-CVS-EOM-CCSD Framework

We report on the implementation and illustrative applications of Dyson orbitals within the recently proposed frozen-core (fc) core-valence separated (CVS) equation-of-motion (EOM) coupled-cluster singles and doubles (CCSD) method, which enables efficient and accurate characterization of core-ionized states.
4 days ago
chemRxiv

Quasi-Diabatic Scheme for Non-adiabatic On-the-fly Simulations

It completely avoids additional theoretical efforts to reformulate the equation of motion from diabatic to adiabatic representation, or construct global diabatic surfaces.
5 days ago
arXiv

qm mm

2 preprints

Towards Sustainable Synthesis of Polyesters: A QM/MM Study of the Enzymes CalB and AfEST

Plastic pollution is causing an immeasurable damage to marine and land eco-systems.
3 days ago
chemRxiv

quantum mechanics

2 preprints

Incorporating action and reaction into a particle interpretation for quantum mechanics -- Dirac case

As a by-product, an appealing possible explanation emerges to another long-standing question, namely why the mathematical formalism of quantum mechanics seems only to be describing fields when measurements generally detect localised particles.
6 days ago
arXiv

The Entropic Dynamics approach to Quantum Mechanics

Entropic Dynamics (ED) is a framework in which Quantum Mechanics is derived as an application of entropic methods of inference.
6 days ago
arXiv

Operator approach in nonlinear stochastic open quantum physics

The reader with basic knowledge of quantum mechanics and quantum noise theory should be able to start using this scheme to his or her own problem of interest.
5 days ago
arXiv

1< b>

2 preprints

N-Acetyl Cysteine Alleviates Coxsackievirus B-Induced Myocarditis by Suppressing caspase-1

Taken together, this study shows that NAC exerts potent anti-CVB effect by inhibiting caspase-1 and viral proteases.
7 days ago
bioRxiv

A case study of bilayered spin-$1/2$ square lattice compound [VO(HCOO)$_2\cdot$(H$_2$O)]

We present the synthesis and a detail investigation of structural and magnetic properties of polycrystalline [VO(HCOO)$_2\cdot$(H$_2$O)] by means of x-ray diffraction, magnetic susceptibility, high-field magnetization, heat capacity, and electron spin resonance measurements.
3 days ago
arXiv

machine learning

2 preprints

Efficient prediction of vitamin B deficiencies via machine-learning using routine blood test results in patients with intense psychiatric episode

Discussion: This study demonstrates that machine-learning can efficiently predict some vitamin deficiencies in patients with active psychiatric symptoms, based on the largest cohort to date with intense psychiatric episode.
6 days ago
medRxiv

Deep Learning and Machine Learning in Hydrological Processes, Climate Change and Earth Systems: A Systematic Review

On the other hand, machine learning methods are already established in the fields, and novel methods with higher performance are emerging through ensemble techniques and hybridization.
5 days ago
Preprints.org

Constrained Multi-Objective Optimization for Automated Machine Learning

Incorporation of multiple objectives and constraints in the model exploration and selection process provides the flexibility needed to satisfy trade-offs necessary in practical machine learning applications.
6 days ago
arXiv

excited states

2 preprints

A Method of Determining Excited-States for Quantum Computation

Thus, low-lying excited-state energies can be calculated using existing hybrid-quantum classical techniques and variational algorithm(s) for determining ground-state.
7 days ago
arXiv

Reaction Rate Of p14N --> 15Ogamma Capture To All Bound States In Potential Cluster Model

Taking into account these results, the total S-factor of the proton capture on 14N and the reaction rates to the ground and five excited states of 15O were determined at temperatures from 0.01 to 10 T9.
4 days ago
arXiv

One-proton and one-neutron knockout reactions from $N = Z = 28$ $^{56}$Ni to the $A = 55$ mirror pair $^{55}$Co and $^{55}$Ni

We present a high-resolution in-beam $\gamma$-ray spectroscopy study of excited states in the mirror nuclei $^{55}$Co and $^{55}$Ni following one-nucleon knockout from a projectile beam of $^{56}$Ni.
3 days ago
arXiv

one pot

2 preprints

Orthogonal Synthesis of Highly Porous Zr-MOFs Assembled from Simple Building Blocks for Oxygen Storage

In this report, a orthogonal MOF synthesis strategy is developed by utilizing the coordination and covalent bonds formation in one-pot where monoacid-based ligands reacted to form ditopic ligands which then assembled into a 3-D MOF with Zr6 clusters.
6 days ago
chemRxiv

Preparation, Characterization, and Application of a Lipophilic Coated Exfoliated Egyptian Blue for Near-Infrared Luminescent Latent Fingermark Detection

An exfoliated Egyptian blue powder coated with cetrimonium bromide was prepared using a simple, one-pot process.
6 days ago
chemRxiv

different proteins

2 preprints

Probing Protein Shelf Lives from Inverse Mean First Passage Times

The rate constants of aggregation of different proteins are calculated from the inverse MFPT, which show an excellent match with the experimentally reported rate constants and those extracted from the ThT/ThS fluorescence data.
6 days ago
chemRxiv

Thermodynamics of Amyloid Fibril Formation from Chemical Depolymerization

Here we use depolymerization by chemical denaturants of amyloid fibrils of two different proteins (PI3K-SH3 and glucagon) at different concentrations and show that the previously applied linear polymerization model is an oversimplification that does not capture the concentration dependence of chemical depolymerization...
3 days ago
chemRxiv

Investigation of the impact of PTMs on the protein backbone conformation

The two main PTM types (N-glycosylation and phosphorylation) have been studied in non-redundant datasets, and then, 4 different proteins were focused, covering 3 types of PTMs: N-glycosylation in renin endopeptidase and liver carboxylesterase, phosphorylation in cyclin-dependent kinase 2 (CDK2), and methylation in actin.
5 days ago
arXiv

novel approach

2 preprints

A novel approach for deducing the mass composition of cosmic rays from lateral densities of EAS particles

From the characteristics of lateral distributions of electrons and muons of simulated EAS, some important EAS observables are extracted by a novel approach, and their CR mass-sensitivity is demonstrated.
7 days ago
arXiv

Discovery of Highly Polymorphic Organic Materials: A New Machine Learning Approach

In this study, a novel approach based on machine learning classification methods is used to predict the likelihood for an organic compound to crystallise in multiple forms.
6 days ago
chemRxiv

Toward an accurate strongly-coupled many-body theory within the equation of motion framework

Non-perturbative aspects of the quantum many-body problem are revised, discussed and advanced in the equation of motion framework.
5 days ago
arXiv

cross sections

2 preprints

Resolving the 11B(p, ${\alpha_0}$) Cross Section Discrepancies between 0.5 and 3.5 MeV

The reaction 11B(p, 3${\alpha}$) is relevant for fields as diverse as material science, nuclear structure, nuclear astrophysics, and fusion science.
7 days ago
arXiv

Measurement of the 3He Spin-Structure Functions and of Neutron (3He) Spin-Dependent Sum Rules at 0.035

The spin-structure functions g_1 and g_2, and the spin-dependent partial cross-section \sigma_{TT} have been extracted from the polarized cross-sections differences, \Delta \sigma_{
4 days ago
arXiv

One-proton and one-neutron knockout reactions from $N = Z = 28$ $^{56}$Ni to the $A = 55$ mirror pair $^{55}$Co and $^{55}$Ni

We present a high-resolution in-beam $\gamma$-ray spectroscopy study of excited states in the mirror nuclei $^{55}$Co and $^{55}$Ni following one-nucleon knockout from a projectile beam of $^{56}$Ni.
3 days ago
arXiv

experimental observations

2 preprints

Observations and Theories of Quantum Effects in Proton Transfer Electrode Processes

First, we review the experimental observations of EQPT, and next, we discuss possible theoretical pictures of the process.
3 days ago
chemRxiv

Surface oscillations and breakup characteristics of a charged droplet in the presence of various time varying functions

A charged droplet can be levitated in the air when suspended in a trap subjected to quadrupole potential.
7 days ago
arXiv

Addressing band-edge-property spatial variations and localized-state carrier trapping and recombination in solar cell numerical modeling

Understanding their effects on a device is necessary in interpreting complex experimental observations and in optimizing the performance of solar cells.
5 days ago
arXiv

b> shows

2 preprints

N-Acetyl Cysteine Alleviates Coxsackievirus B-Induced Myocarditis by Suppressing caspase-1

Taken together, this study shows that NAC exerts potent anti-CVB effect by inhibiting caspase-1 and viral proteases.
7 days ago
bioRxiv

Universal fluctuations in the bulk of Rayleigh-B'enard turbulence

We present an investigation of the root-mean-square (rms) temperature $\sigma_T$ and the rms velocity $\sigma_w$ in the bulk of Rayleigh-B\'enard turbulence, using new experimental data from the current study and experimental and numerical data from previous studies.
3 days ago
arXiv

Orbit design and thruster requirement for various constant-arm space mission concepts for gravitational-wave observation

In previous papers, we have addressed the issues of orbit design and thruster requirement for the constant arm versions of AMIGO (Astrodynamical Middle-frequency Interferometric Gravitational-wave Observatory) mission concept and for the constant arm GW (gravitational wave) mission concept of AIGSO (Atom Interferometric Gravitational-wave Space Observatory).
4 days ago
arXiv

molecular mechanics

2 preprints

Towards Sustainable Synthesis of Polyesters: A QM/MM Study of the Enzymes CalB and AfEST

Here we compare in detail the catalytic mechanisms for polycaprolactone synthesis by the enzymes Archaeoglobus fulgidus carboxylesterase (AfEST) and Candida antarctica lipase B (CalB) by performing Quantum mechanics calculations and Quantum Mechanics/Molecular Mechanics Molecular Dynamics simulations.
3 days ago
chemRxiv