Born-Oppenheimer Molecular Dynamics Research Articles

FLi4X4− (X = Cl, Br, I): Superhalogen Anions with Planar Tetracoordinate Fluorine

The concept of superhalogen was proposed for more than 40 years, and it has never been associated with planar tetracoordinate fluorine (ptF) species. In this work, using Li as the ligands and Cl, Br, I as the auxiliary atoms, we have designed the star-like D4h FLi4X4− (X = Cl, Br, I) clusters, which contain the ptF at the centers. They are all global minima (GMs) based on unbiased searches on the potential energy surfaces. Born–Oppenheimer molecular dynamics (BOMD) simulations suggest that these ptF structures are robust against dissociation at room temperature. Chemical bonding analyses indicate that there are four lone pairs (LPs) for ptF, three LPs for each X atom, and four 3c-2e Li–X–Li σ bonds. The stabilities of these ptF clusters are dominated by multicenter ionic bonding, rather than the σ aromaticity. Interestingly, these ptF species have large first vertical detachment energies (7.37, 6.94, and 6.30 eV). According to the definition of superhalogen, they can be viewed as superhalogen anions. The current work builds an important link between superhalogen and ptF chemistry.

Photochemical and Collision-Induced Cross-Linking of Asp, Glu, Asn, and Gln Residues in Peptide-Nitrile Imine Conjugate Ions in the Gas Phase.

Peptide conjugates furnished with a 2,5-diaryltetrazolecarbonyl tag at the C-terminal lysine, which we call peptide-tet-K, were found to undergo efficient cross-linking of Asp, Glu, Asn, and Gln residues to transient nitrile-imine intermediates produced by photodissociation and collision-induced dissociation (CID) of the tetrazole ring in gas-phase ions. UV photodissociation (UVPD) at 213 nm achieved cross-linking conversion yields of 37 and 61% for DAAAK-tet-K and EAAAK-tet-K, respectively. The yields for NAAAK-tet-K and QAAAK-tet-K were 29 and 57%, respectively. Even higher cross-link yields were found for CID-MS3 of stable denitrogenated ions, (peptide-tet-K-N2 + H)+, that were in the 69-83% range. Different types of cross-links were distinguished by CID-MSn that showed a distinct series of backbone fragment ions, loss of N-terminal groups, and loss of phenylhydrazine from the modified nitrile imines. The Asp and Glu side-chain carboxyl groups were major participants in cross-linking that resulted in proton and oxygen transfer to the nitrile imine group. Other types of cross-linking involved Asn and Gln CONH2 groups and backbone amides. Cyclic ion mobility-mass spectrometry was used to separate NAAAK-tet-K and QAAAK-tet-K conformers and products of their collision-induced denitrogenation. Linear nitrile-imine and cross-linked ion structures were identified by comparing the experimental collision cross sections (CCSexp) to those for structures obtained by combined Born-Oppenheimer molecular dynamics and density functional theory (DFT) calculations. The formation of cross-links was found to be energetically favorable and involved proton-facilitated nucleophilic attack at the nitrile-imine carbon atom.

Dual structural fluxionality in the copper borozene complex Cu3B8-: A two-layered molecular rotor.

Doubly aromatic B82-, a borozene analog of benzene (C6H6) due to their similar π bonding, can be considered an ideal base for multi-layered molecular rotors. Here, we theoretically constructed the copper borozene complex Cu3B8- to investigate its stability and structural fluxionality. The lowest energy isomers consist of two-layered configurations: a B8 molecular wheel and a triangular Cu3 motif that either stands upright or lies flat above the B8 wheel. Both configurations exhibit structural fluxionality, as indicated by the free rotation of Cu3 with respect to the B8 molecular wheel, confirmed by Born-Oppenheimer molecular dynamics simulations even at low temperatures. This fluxional behavior is associated with an ultra-soft vibrational mode of Cu3 (less than 10.0cm-1) and a negligible rotational barrier of 0.01 kcal/mol. Notably, high simulated temperatures cause irregular interconversion between the standing and lying orientations of Cu3 without regularity. Chemical bonding analysis confirmed that charge transfer from Cu3 to the B8 wheel renders Cu3B8- a typical copper borozene complex, [Cu3+][B82-], where B82- has six delocalized π and σ electrons. This electron delocalization contributes to a dilute and continuous electron cloud that underpins the dynamic behavior of the Cu3 trimer.

Ab Initio Molecular Dynamics Studies of Stacked Adenine–Thymine and Guanine–Cytosine Nucleic Acid Base Pairs in Aqueous Solution

Ab initio MD studies have been performed on stacked adenine–thymine (A–T) and guanine–cytosine (G–C) nucleobase pairs solvated in water using Born–Oppenheimer molecular dynamics. These two systems have been analyzed using RDF, SDF, angle–distance CDF (combined distribution functions), plane projection analysis, hydrogen bond analysis, and non–covalent interaction (NCI) plots. The stacking property studies have shown that the molecular orientation of the A–T pair is completely opposite to that of the G–C pair though the center of mass distance between the two molecules is similar. The G–C pair shows significantly more stability in water than the A–T system does. RDF analyses show that the –NH– group and carbonyl groups show predominant interaction with water molecules. Water molecules are found to be most in numbers around the cytosine molecule and least around the adenine molecule. Hydrogen bonding studies show that the guanine molecule forms the highest number of hydrogen bonds with water molecules. On the other hand, the hydrogen atom attached to the –NH– group of adenine molecule shows the longest mean H–bond lifetime with water oxygen atoms. NCI interactions calculated through the ab initio method help us to visualize the [Formula: see text]-electron stacking and H–bonding between aromatic nucleobases and water molecules. A great shift in bond polarity and interaction intensity in different functional groups is observed for the nucleobases going from individually solvated molecules to paired states.

Photochemical and Collision-Induced Cross-Linking in Stereochemically Distinct Scaffolds of Peptides and Nitrile Imines in Gas-Phase Ions.

Intramolecular cross-linking between peptides and nitrile-imine intermediates was studied in stereochemically distinct conjugates in which the reacting components were mounted on cis-1,2-cyclohexane and trans-1,4-cyclohexane scaffolds that we call 1,2-s-peptides and 1,4-s-peptides, respectively. The nitrile-imine intermediates were generated by N2 loss from 2,5-diaryltetrazole tags upon UV-photodissociation at 213 and 250 nm or by collision-induced dissociation, and further interrogated by CID and UVPD-MS3. Peptide fragment ion series originating from linear structures and macrocyclic cross-links were distinguished and used to quantify the cross-linking yields. The yields in MS2 varied between 27% for AAAG conjugates to 78% for GAAAK conjugates, depending on the peptide sequence. The CID-MS3 yields were in a 57-97% range, depending on the peptide sequence. Structures of 1,2-s-peptide and 1,4-s-peptide ions as well as several of their nitrile-imine intermediates and cross-links were investigated by high-resolution cyclic ion mobility in combination with Born-Oppenheimer molecular dynamics and density functional theory calculations. Matches between the experimental and calculated collision cross sections and ion relative Gibbs energies were used to assign peptide structures. Peptide conjugates C-terminated with Gly and Lys residues underwent cross-linking by the carboxyl group, as established by MS3 sequencing and corroborated by carboxyl blocking experiments that lowered the cross-linking yields. Peptide conjugates C-terminated with Arg also cross-linked via the side-chain guanidine group. A notable feature of the 1,4-s-peptide ions was the participation of low-energy twist-boat cyclohexane conformers that was enforced by strong hydrogen bonds between the peptide and nitrile imine.

Molecular Association and Reactivity of the Pyridine Dimer Cation.

A recent experimental report has identified the formation of the C-N hemibonded pyridine dimer cation following vacuum ultraviolet near-threshold photoionization [J. Phys. Chem. Lett., 2021, 12, 4936-4943]. Herein, the dynamics and consequent reactivity of the pyridine dimer cation were investigated employing Born-Oppenheimer molecular dynamics (BOMD) simulations. An antiparallel π-stacked pyridine dimer in the neutral ground state is transformed into a noncovalently interacting C-H···N hydrogen-bonded structure which can lead to proton transfer in the cationic state. Additionally, C-N- and N-N-bonded adducts were formed in the cationic state. Further, metastable C-H···H-C-bonded cationic species was observed, which rearranged to an N-N bonded adduct. In contrast to the experimental observation, migration of the proton to the α position was not observed in the C-N bonded adduct owing to a high barrier of about 2 eV. The observed trends in the molecular association, proton transfer, and the formation of C-N and N-N bonded adducts are a consequence of the roaming dynamics of one pyridine moiety over the other in the cationic state.

Two-Step Noncatalyzed Hydrolysis Mechanism of Imines at the Air-Water Interface.

The hydrolysis of imines has long been assumed to be their main atmospheric fate, based on early studies in the field of organic chemistry. However, the hydrolysis mechanism and kinetics of atmospheric imines remain unclear. Here, an advanced Born-Oppenheimer molecular dynamics method was employed to investigate the noncatalyzed hydrolysis mechanism and kinetics at the air-water interface by selecting CH2NH as a model molecule. The results indicate that CH2NH exhibits a pronounced surface preference. The noncatalyzed hydrolysis of CH2NH follows a unique two-step reaction mechanism involving first proton transfer and then OH- transfer through the water bridge at the air-water interface, in contrast to the traditional one-step mechanism. The calculated reaction rate for the rate-determining step is 3.32 × 105 s-1, which is 2 orders of magnitude greater than that of the bulk phase. In addition, the involvement of the interfacial electric field further enhances the reaction rate by approximately 3 orders of magnitude. The noncatalyzed hydrolysis rate at both the air-water interface and the bulk phase is higher than that of the possible acid-catalyzed one, clarifying noncatalyzed hydrolysis as the dominant mechanism for CH2NH. This study elucidates that the noncatalyzed hydrolysis of atmospheric imines is feasible at the air-water interface and that the revealed unique two-step hydrolysis mechanism has significant implications in atmospheric and water environmental chemistry.

Probing the Role of Solvent Configurations and Local Electric Fields on HX (X = F, Cl, Br and I) Dissociation in Water Clusters.

The acidity of hydrohalic acids increases down the group, with HF and HI being the weakest and strongest acids. Electronic structure calculations suggest that the critical electric fields required for the dissociation of HF, HCl, HBr, and HI are 347, 193, 163, and 153 MV cm-1, respectively, which are proportional to their corresponding pKa values and emphasize that in these systems the bond dissociation energy determines the pKa. The solvent configuration plays a significant role in the acid dissociation process, which is illustrated by a particular configuration of three water molecules around HX and favors dissociation of only HBr, even though the critical electric field required for the dissociation of HI is lower than that of HBr, as depicted in the graphical abstract. Further, the Born-Oppenheimer molecular dynamics (BOMD) simulations suggest that the spontaneity of HX dissociation depends on both the solvent configuration and thermal fluctuations, which hold higher significance in the case of weaker acids. In general, it was observed that the solvent electric field required for the acid dissociation process is marginally lower at higher temperatures.

Structure-Activity relationship of 5‑butyl‑4,6-dimethyl-2-{[4-(o-fluorophenyl)-1-piperazinyl]-2-oxoethyl}-pyrrolo[3,4-c]pyrrole-1,3(2H,5H)‑dione: An experimental and theoretical study

Synthesis of 5‑butyl‑4,6-dimethyl-2-{[4-(o-fluorophenyl)-1-piperazinyl]-2-oxoethyl}-pyrrolo[3,4-c]pyrrole-1,3(2H,5H)‑dione 3 is reported. The compound was obtained by direct alkylation of 3,4-pyrrolodicarboximide 1 with (1-chloroacetyl-4-(o-fluorophenyl)piperazine) 2 in DMF. Its physico-chemical features were characterized by 1H NMR, 13C NMR, FT-IR, MS spectra, and elemental analysis. Single-crystal X-ray diffraction was also recorded. A colorimetric inhibitor screening assay was used to determine its inhibitory potency towards COX-1 and COX-2. It was found that the compound exhibits anti-inflammatory activity higher than the reference structure – Meloxicam (MXM). According to the experimental results, the tested compound inhibited the activity of COX-1 and COX-2 respectively. In the next step, molecular docking was performed to estimate the binding affinity of compound 3 and commercially available reference compounds for COX-1/COX-2 enzymes. It was found that the binding affinity of 3 is higher than for the reference compounds. Quantum Theory of Atoms In Molecules (QTAIM) and Reduced Density Gradient (RDG) methods were used to reveal non-covalent interactions present in the COX-1/COX-2 binding pocket. Finally, Born-Oppenheimer molecular dynamics (BOMD) based on semiempirical forces was carried out to gain insight into the dynamic features of the studied complexes and confirmed the fact that the weak hydrogen bonds play the most important role in stabilizing the ligand conformation for the studied COX-2 complexes with compound 3 and Rofecoxib.

CB11S3+: A Triangular Boron-Based Cluster with One Planar Tetracoordinate Carbon at Its Edge.

Boron-based clusters containing planar tetracoordinate carbon (ptC) are unique and scarce. Isoelectronic-replacing after proper vulcanization is an effective strategy to obtain the ptC based on the B12 cluster. Herein we report computational evidence for a ternary CB11S3+ (C2v, 1A1) cluster, which possesses a concentric double-triangle structure containing one ptC atom at the peripheral edge. The unbiased structural explorations of potential energy surfaces and high-level CCSD(T) calculations indicate that the ptC CB11S3+ cluster is a true global minimum. Born-Oppenheimer molecular dynamics (BOMD) simulations reveal that it is dynamically stable against isomerization and decomposition. Chemical bonding analysis reveals that three delocalized π bonds endow the π aromaticity to the CB11 unit of CB11S3+. In addition, the strong S → B π back-bonding is also conducive to the stability of CB11S3+. The current findings offer opportunities for further boron-based ptC clusters.

Knotted or unknotted? A theoretical quantum protocol for luminescence simulation of metallo-supramolecular knots

Entangled structures are topological architectures often observed not only in the macroscopic world, but also at the molecular level with many examples in biological systems (DNA, RNA). In recent decades, these fascinating entities have aroused considerable interest among chemists with the advent of metallo-supramolecular knots. Notwithstanding the burgeoning of such metal complexes in literature, their use as luminescent emitters as well as systematic studies on their luminescence properties are still extremely limited. In view of this, a theoretical DFT protocol dedicated to luminescence profile simulations of these peculiar “entwined” species is highly desirable. In this work, we propose a robust and affordable DFT computational workflow able to recreate meticulously the emission band-shape of different metallo-supramolecular knots. As a result of a preparatory DFT benchmark, we decided to use HSEH1PBE/LanL2DZ level via Born-Oppenheimer molecular dynamics to explore the change in the coordination environment around the metal centers in the excited state (S1). Thereupon, a detailed recruiting of TD-DFT functionals recommended the mPW3PBE/LanL2DZ level as the most precise and transferable method to model accurately metallo-supramolecular knots emission spectra as metal ions, internal spacers and interlocking modes vary.

IRMPD spectroscopy of deprotonated selenocysteine - The 21st proteinogenic amino acid

The effect of deprotonation on the structure and stability of the 21st proteinogenic amino acid selenocysteine, generated as bare deprotonated species by electrospray ionization, has been investigated by infrared multiple photon dissociation (IRMPD) spectroscopy over an extended frequency range (700-3600 cm−1), encompassing both the fingerprint and X–H (X = C, N, O) stretching ranges. IRMPD spectra, interpreted by anharmonic DFT calculations, provide evidence of a thermally averaged ion population of two types of low-lying canonical conformers deprotonated at the selenol (Se–H) group and involved in different H-bonding motifs.The broadened and diffuse band structures observed in the H-stretching range are well interpreted by Born-Oppenheimer molecular dynamics computations that provide a valuable description of the flexible backbone arrangements of Sec and of the proton sharing dynamics in the Se–HO and Se–HN moieties.Other prototropic isomers, deprotonated at the carboxylic group or with a zwitterionic structure, should not be significantly populated, according to their higher free energy and calculated IR spectra inconsistent with experimental evidence.

A first principles study of stability, electronic and thermoelectric characteristics of novel high temperature half- heusler alloys ScAgX (X=Si,Ge,Sn)

To meet the ever-increasing renewable energy demand Half- Heusler (HH) materials can be a potential candidate. Heusler materials are seeking popularity as efficient high-temperature thermoelectric materials. Here we systematically investigated the structural, electronic, mechanical and thermoelectric properties of novel HH compounds ScAgX (X = Si,Ge,Sn) in the framework of the first principles approach. These materials are found to be chemically, mechanically and dynamically stable. Born-Oppenheimer molecular dynamics simulations (BOMD) verify the thermal stability of these materials from 300 K to 1100 K. The semiconducting nature of these materials is confirmed by the electronic band structure. ScAgX (X = Si,Ge,Sn) have an indirect band gap of 0.37 eV, 0.42 eV and 0.38 eV respectively. A high value of Seebeck coefficient of 6351 μV/K, 6955 μV/K and 6558 μV/K has been obtained at room temperature. ScAgSi shows a high value of electrical conductivity (∼106 S/m) among these compounds at room temperature. The calculated value of the figure of merit (ZT) of ScAgX (X = Si,Ge,Sn) is 0.12, 0.08 and 0.16 at 1100 K respectively. Our present investigation shows that these materials can be a potential candidate for high-temperature thermoelectric power generation.

Insights into the catalytic effect of atmospheric organic trace species on the hydration of Criegee intermediates

The bimolecular reactions between Criegee intermediates (CIs) and atmospheric trace species have been extensively investigated, with a particular focus on the reaction with water, while the catalytic role of atmospheric organic compounds in hydration reactions was often neglected. In this study, we employed quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations to investigate the catalytic effects of atmospheric organic amines, organic acids, and alcohols on the hydration reactions of CIs in the gas phase and at the gas-liquid interface. The catalytic reactions were found to follow a cyclic catalytic structure and a stepwise reaction mechanism. Gas-phase studies revealed that organic acids exhibited stronger catalytic effects compared to amines and alcohols, and the catalytic efficiency of amines and alcohols was similar to those of single water molecule. In addition, the catalytic reaction barriers of organic acids and alcohols were positively correlated with their gas-phase acidity (R2 = 0.94 to 0.97). A negative correlation was observed between the catalytic reaction barrier of amines and their gas-phase basicity (R2 = 0.84 to 0.90) and proton affinity (R2 = 0.84 to 0.92). At the gas-liquid interface, organic acids promoted the formation of hydroxyethyl hydroperoxide (HEHP, CH3CH(OH)(OOH)), organic acid ions, and H3O+, whereas the catalytic hydration of CIs by organic amines resulted in the formation of CH3CH(OH)OO and amine ions. Both HEHP and CH3CH(OH)OO can be further decomposed to form OH and HO2, or participate in new particles formation as precursors. This study complements the research gap on the reaction of CIs with water, providing valuable insights into the atmospheric sources of HEHP and HOx as well as the formation of secondary organic aerosols (SOAs).

Indazole-5-amine (AIA) as competing corrosion coating to Benzotriazole (BTAH) at the interface of Cu: A DFT and BOMD case study

This study compares three organic compounds—benzotriazole (BTAH), imidazole (IM), and indazole-5-amine (AIA)—as corrosion inhibitors for copper substrates. Using Density Functional Theory (DFT) and Born-Oppenheimer Molecular Dynamics (BOMD) calculations, it identifies AIA as a promising and cost-effective alternative to the toxic BTAH. The adsorption strength on Cu(100) surfaces is ranked AIA>BTAH>IM for both neutral and deprotonated forms. These findings are supported by electronic parameter studies, including Bader charge analysis, density of states (DOS), charge density differences (CDD), and frontier molecular orbital analysis. AIA shows the best adsorption in a parallel orientation at the top site. Packing studies reveal that hydrogen bonding stabilizes the interaction energies within self-assembled AIA aggregates. Organometallic complexation studies reveal that deprotonated BTAH exhibits higher interaction energy with a single Cu atom compared to AIA when bonded through the carbon end, consistent with the findings from BOMD studies. However, on periodic Cu surfaces, AIA outperforms BTAH molecules as seen from adsorption energies. This investigation highlights AIA’s potential as a superior and more economical corrosion inhibitor for copper.

Achieving High Substitutional Incorporation in Mn-Doped Graphene.

Despite its broad potential applications, substitution of carbon by transition metal atoms in graphene has so far been explored only to a limited extent. We report the realization of substitutional Mn doping of graphene to a record high atomic concentration of 0.5%, which was achieved using ultralow-energy ion implantation. By correlating the experimental data with the results of ab initio Born-Oppenheimer molecular dynamics calculations, we infer that direct substitution is the dominant mechanism of impurity incorporation. Thermal annealing in ultrahigh vacuum provides efficient removal of surface contaminants and additional implantation-induced disorder, resulting in Mn-doped graphene that, aside from the substitutional Mn impurities, is essentially as clean and defect-free as the as-grown layer. We further show that the Dirac character of graphene is preserved upon substitutional Mn doping, even in this high concentration regime, making this system ideal for studying the interaction between Dirac conduction electrons and localized magnetic moments. More generally, these results show that ultralow energy ion implantation can be used for controlled functionalization of graphene with substitutional transition-metal atoms, of relevance for a wide range of applications, from magnetism and spintronics to single-atom catalysis.

Robust and effective ab initio molecular dynamics simulations on the GPU cloud infrastructure using the Schrödinger Materials Science Suite

Ab initio Born-Oppenheimer molecular dynamics (AIMD) is a valuable method for simulating physico-chemical processes of complex systems, including reactive systems, and for training machine learning models and force fields. Speed and stability issues on traditional hardware preclude routine AIMD simulations for larger systems and longer timescales. We postulate that any practically useful AIMD simulation must generate a trajectory of a minimum 1000 MD steps a day on a moderate cloud resource. In this work, we implement a computing workflow that enables routine calculations at this throughput and demonstrate results for several non-trivial atomistic dynamical systems. In particular, we have employed the GPU implementation of the Quantum ESPRESSO code which we will show increases AIMD productivity compared to the CPU version. In order to take advantage of transient servers (which are more cost and energy effective compared to the stable servers), we have implemented automatic restart/continuation of the AIMD runs within the Schrödinger Materials Science Suite. Finally, to reduce simulation size and thus reduce compute time when modeling surfaces, we have implemented a wall potential constraint. Our benchmarks using several reactive systems (lithium anode surface/solvent interface, hydrogen diffusion in an iron grain boundary) show a significant speed up when running on a GPU-enabled transient server using our updated implementation.

Nitrous Acid (HONO) Dissociation on the Water and Ice Surface: An Ab Initio Molecular Dynamics Study.

In the atmosphere, the photodissociation of HONO is a significant source of OH radicals after ozone. In the present study, using Born-Oppenheimer molecular dynamics, we showed that HONO can dissociate on ice and water surfaces without light. In addition, the dissociation time of HONO is found to be much less on the ice surface compared to the same time on the water droplets.

Nucleoside Cation Radicals: Generation, Radical-Induced Hydrogen Atom Migrations, and Ribose Ring Cleavage in the Gas Phase.

Nucleoside ions that were furnished on ribose with a 2'-O-acetyl radical group were generated in the gas phase by multistep collision-induced dissociation of precursor ions tagged with radical initiator groups, and their chemistry was investigated in the gas phase. 2'-O-Acetyladenosine cation radicals were found to undergo hydrogen transfer to the acetoxyl radical from the ribose ring positions that were elucidated using specific deuterium labeling of 1'-H, 2'-H, and 4'-H and in the N-H and O-H exchangeable positions, favoring 4'-H transfer. Ion structures and transition-state energies were calculated by a combination of Born-Oppenheimer molecular dynamics and density functional theory and used to obtain unimolecular rate constants for competitive hydrogen transfer and loss of the acetoxyl radical. Migrations to the acetoxyl radical of ribose hydrogens 1'-H, 2'-H, 3'-H, and 4'-H were all exothermic, but product formation was kinetically controlled. Both Rice-Ramsperger-Kassel-Marcus (RRKM) and transition-state theory (TST) calculations indicated preferential migration of 4'-H in a qualitative agreement with the deuterium labeling results. The hydrogen migrations displayed substantial isotope effects that along with quantum tunneling affected the relative rate constants and reaction branching ratios. UV-vis action spectroscopy indicated that the cation radicals from 2'-O-acetyladenosine consisted of a mixture of isomers. Radical-driven dissociations were also observed for protonated guanosine, cytosine, and thymidine conjugates. However, for those nucleoside ions and cation radicals, the dissociations were dominated by the loss of the nucleobase or formation of protonated nucleobase ions.

Relaxation of the 2a1 ionized water dimer: An interplay of intermolecular Coulombic decay (ICD) and proton transfer processes.

This article investigates the relaxation dynamics of the ionized 2a1 state of a water molecule within a water dimer. The study was motivated by findings from two previous pieces of research that focused on the relaxation behaviors of the inner-valence ionized water dimer. The present study discloses an observation indicating that water dimers display specific fragmentation patterns following inner-valence ionization, depending on the position of the vacancy. Vacancies were created in the 2a1 state of the proton-donating water molecule (PDWM) and proton-accepting water molecule (PAWM). Utilizing Born-Oppenheimer molecular dynamics simulations, the propagation of the 2a1 ionized state was carried out for both scenarios. The results revealed proton transfer occurred when the vacancy resided in the PDWM, accompanied by the closing of decay channels for O-H bond distance (RO-H) > 1.187Å (matching Richter et al.'s findings). Conversely, when vacancy was on PAWM, we observed no closing of decay channels (aligning with Jahnke et al.'s findings). This difference translates to distinct fragmentation pathways. In PDWM cases, 2a1 state ionization leads to H3O+ -OH• formation. In contrast, PAWM vacancies result in decay pathways leading to H2O+-H2O+ products.