We perform a comprehensive investigation on the geometry, stability, aromaticity, bonding nature, and potential energy surface of low-lying isomers of planar BnC2 (n = 3–8) at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. The geometries of lowest-energy isomers of CnB2 (n = 3–8) clusters are similar to the results of Wang and Zeng, respectively. CnB2 (n = 3–6) clusters are analogous to pure boron clusters in structure. Interestingly, the lowest-energy isomers of BnC2 (n = 3–8) clusters undergo polycyclic to wheel-type structure transition as the number of boron atom increases. Energy analysis reveals that BnC2 clusters with even n have relatively higher stability. The valence molecular orbital (VMO), electron localization function (ELF), and Mayer bond order (MBO) are used to reveal the bonding feature of BnC2 (n = 3–8) isomers. The aromaticity of B6C2 and B8C2 is discussed in terms of VMO, ELF, adaptive natural density partitioning (AdNDP), and nucleus-independent chemical shift (NICS) analyses. Some B3C2 and B5C2 isomers with large thermodynamic and kinetic stability are predicted at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level and observable in laboratory.Graphical abstractHighlights► The lowest-energy isomers of even-n BnC2 clusters have high stability. ► BnC2 (n = 3–8) clusters exhibit polycyclic to wheel-like structure transition. ► The growth pattern and bonding nature of BnC2 (n = 3–8) are revealed. ► The thermodynamic and kinetic stability of BnC2 (n = 3–8) is examined. ► The aromaticity of some BnC2 isomers (n = 3–8) is analyzed and discussed.

Poly(ethylene glycol) dimethyl ether (PEGDME) polymers are widely used as drug solid dispersion reagents. They can cause the amorphization of drugs and improve their solubility, stability, and bioavailability. However, the mechanism about why amorphous PEGDME 2000 polymer is highly stable is unclear so far. Molecular dynamics (MD) simulation is a unique key technique to solve it. In the current work, we systematically investigate structure, aggregate state, and thermodynamic and kinetic behaviors during the phase-transition processes of the PEGDME polymers with different polymerization degree in terms of MD simulations. The melting and glass-transition temperatures of the polymers are in good agreement with experimental values. The amorphous PEGDME2000 exhibits high stability, which is consistent with the recent experiment results and can be ascribed to a combination of two factors, that is, a high thermodynamic driving force for amorphization and a relatively low molecular mobility.Keywords: configurational entropy; glass transition; melting; molecular mobility; phase transition; polymerization degree; stability;

The structures, stabilities, and potential energy surfaces (PESs) of the low-lying isomers of planar BnN (n = 1–6) clusters are searched at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. The lowest-energy structures (1a–6a) of planar BnN (n = 1–6) are located. It is worthy to note a structural transition occurring in the series of BnN (n = 1–6) clusters upon increase of the boron content from n = 3 to n = 4. The evolution of the binding energy per atom, incremental binding energy, and second order difference of total energy with the size of BnN reveals that the lowest-energy isomers 2a (B2N) and 5a (B5N) are highly stable. Results demonstrate that the stability of lowest-energy isomers of BnN (n = 1–6) is attributed to the delocalized π, σ-radial, and σ-tangential molecular orbitals (MOs) interactions. The isomers of BnN (n = 4–6) with planar multicoordinate boron or nitrogen are unfavorable in energy. The double aromaticity of isomer 3d of B3N is discussed in terms of valence molecular orbital, electron localization function (ELF) and adaptive natural density partitioning (AdNDP), and NICS analyses. Interestingly, some isomer pairs can be transferred directly to each other by two or three isomerization channels. Some isomers of BnN with large thermodynamic and kinetic stability are predicted in terms of their total energies and potential energy surfaces, which is important for future experimental studies.Graphical abstractHighlights► The lowest-energy structures (1a–6a) of planar BnN (n = 1–6) are obtained. ► BnN (n = 1–6) exhibit linear to polycyclic structure transition. ► BnN with n = 2 and 5 have relatively higher stability. ► The growth pattern and bonding nature of BnN (n = 1–6) are revealed. ► The thermodynamic and kinetic stability of BnN (n = 1–6) is examined.

We have applied MD simulation method to investigate the structure, phase transition, and nucleation of KI nanoparticles confined in zigzag single-wall carbon nanotubes ((n, 0)-SWNTs). SWNTs are approximately handled to be rigid. The ion–ion interactions are represented by Born–Mayer–Huggins’ potential and the KI-SWNT interactions are described by Lennard–Jones potential. The total energies, structures, and Lindemman indices reveal the feature of phase transition for KI nanoparticles confined in (n, 0)-SWNTs. The nucleation analysis is carried out by classical nucleation theory. Results demonstrate that the structures of the confined (KI)N nanoparticles are very sensitive to the length of KI nanoparticles and tube diameter and the confined KI nanoparticles have multishelled or FCC structures. Interestingly, on the cross section perpendicular to the tube axis, the arrangement of K+ and I− ions exhibits some quasi-five-membered rings, which may be related to geometrical match between KI ionic radii and tube diameter, and confining effect of SWNT. In addition, some important thermodynamic and dynamic parameters are derived and compared with available experimental and calculated results.Graphical abstractHighlights► The structures and properties confined KI nanoparticles are studied. ► The confined KI nanoparticles may have FCC or multishelled structure. ► The outermost layer of the confined (KI)N exhibits more order than the core. ► Some important thermodynamic and dynamic parameters are estimated.

The geometrical structures, potential energy surfaces, stabilities, and bonding characteristics of low-energy isomers for planar C4B2 and C2B4 are systematically investigated at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. Isomers 1a (C2h, 1Ag1Ag) and 2a (D2h, 1Ag1Ag) with belt-like geometries are the lowest-energy structures of C4B2 and C2B4, respectively, and their structures tend to be similar to those of B6, CB5, and C3B3 clusters. For CxB6-x (x = 1–6) clusters, an interesting planar-to-linear structural transition occurs at x = 1 and 2. The σ-radial, σ-tangential, and delocalized π molecular orbitals are favorable to stabilizing structures of lower-energy isomers of C4B2 and C2B4 based on the NBO and molecular orbital analyses. The lowest-energy isomers of C4B2 and C2B4 are stable both thermodynamically and kinetically at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level and detectable in experiment, which is significant for future experimental studies of C4B2 and C2B4.

The geometries, stabilities, and potential energy surfaces of possible isomers of BnP2 (n = 1–7) are explored and investigated at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. Many planar structures for the possible isomers of BnP2 (n = 1–7) and transition states are located. The lowest-energy structures (1a–7a) of BnP2 exhibit belt-like growth feature with two phosphorus atoms capped to two terminal B-B edges of Bn unit. The lowest-energy structures B2P2(2a), B4P2(4a), and B6P2(6a) are more stable than their neighbors. Especially, the lowest-energy isomer (4a) of B4P2 has exceptional stability. Results from molecular orbital analysis suggest that the formation of the delocalized π, the σ-radial, and σ-tangential MOs is favorable to stabilizing the structures of lowest-energy isomers (1a–7a) of BnP2. In addition, results from molecular orbital and nucleus independent chemical shift demonstrate that BP2 and B7P2 may have aromaticity. Importantly and interestingly, the lowest-energy isomers (2a, 3a, 4a, 5a, and 6a) of BnP2 (n = 2–6) are stable both thermodynamically and kinetically at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level and may be observable in laboratory, which is helpful for further experimental studies of BnP2.

A MD simulation method is used to simulate the melting and freezing of Au−Pt nanoparticles confined in armchair single-walled carbon tubes ((n,n)-SWNTs), applying the second-moment approximation of the tight-binding potentials for metal−metal interactions and Lennard-Jones potential for the metal−carbon interactions. The carbon atoms on the SWNTs are taken to be fixed. The structures, total energies, Lindemman indices, and radial and axial density distributions are used to examine the behaviors of melting and freezing for Au−Pt nanoparticles confined in (n,n)-SWNTs. The nucleation analysis is carried out in terms of classical nucleation theory. The simulation results demonstrate that the solid Au−Pt clusters confined within (n,n)-SWNTs have multishell structures, even in a melted cluster. In addition, for the confined Au−Pt nanoparticles, Pt atoms tend to stay at the position close to the SWNT wall, which is different from free Au−Pt nanoparticles. Simulation results reveal that SWNTs and compositions of nanoparticles have significant effects on the structures and physical properties of the confined Au−Pt nanoparticles. On the other hand, some important thermodynamic and dynamic parameters are estimated based on MD simulations and compared with available theoretical and experimental results.

We have systematically explored and investigated the geometrical structures, stability, growth pattern, bonding character, and potential energy surface (PES) of the possible isomers of each cluster for planar BnP (n = 1 ∼ 7) at the CCSD(T)/6-311+;G(d)//B3LYP/6-311+G(d) level. A large number of planar structures for the possible isomers of BnP (n = 1 ∼ 7) and transition states are located. Isomers 1a ∼ 7a of BnP are the lowest-energy structures and 2a, 4a, as well as 6a are more stable than their neighbors. For the lowest-energy structures (1a ∼ 7a) of BnP, P atom lies at the apex and tends to form two B-P bonds with boron atoms. They exhibit planar zigzag growth feature or approximately spherical-like growth pattern. Results from molecular orbital analysis demonstrate that the formation of the delocalized π MOs and the σ-radial and σ-tangential MOs plays a critical role in stabilizing the structures of lowest-energy isomers (2a ∼ 7a) of BnP. Importantly, isomers 3a, 3c, 3d, 4a, 4b, 5b, and 5c of BnP are stable both thermodynamically and kinetically at the CCSD(T)/6-311+G(d)// B3LYP/6-311+G(d) level and detectable in laboratory, which is valuable for further experimental studies of BnP.

We investigate theoretically the structures and second-order nonlinear optical (NLO) responses (first hyperpolarizabilities) of 15 trisaza-bridged (36) fulleroids (series-A) and 15 triborane-bridged (36) fulleroids (series-B). 3A has smaller transition energy and smaller ground state dipole moment, resulting in relatively larger static first hyperpolarizability (10647 au). Most trisaza-bridged (36) fulleroids have larger β values than the corresponding triborane-bridged (36) fulleroids. The f0 and Δμ remain stable values when substituents R change for series-A except 2A and 5A (for series-B except 5B and 10B) and β values are proportional to ΔE-3, which implies that the β values for series-A and series-B follow the two-level model. Results demonstrate that a proper bridge and lower transition energy ΔE are more favorable to enlarging first hyperpolarizabilities of series-A and series-B. In addition, the frequency-dependent SHG and EOPE are also estimated and discussed. The current work can stimulate experimentalists to synthesize novel NLO materials designed in this work.

Human P450 protein CYP2C9 is one of the major drug-metabolizing isomers, contributing to the oxidation of 16% of the drugs currently in clinical use. To examine the interaction mechanisms between CYP2C9 and proton pump inhibitions (PPIs), we used molecular docking and molecular dynamics (MD) simulation methods to investigate the conformations and interactions around the binding sites of PPIs/CYPP2C9. Results from molecular docking and MD simulations demonstrate that nine PPIs adopt two different conformations (extended and U-bend structures) at the binding sites and position themselves far above the heme of 2C9. The presence of PPIs changes the secondary structures and residue flexibilities of 2C9. Interestingly, at the binding sites of all PPI–CYP2C9 complexes except for Lan/CYP2C9, there are hydrogen-bonding networks made of PPIs, water molecules, and some residues of 2C9. Moreover, there are strong hydrophobic interactions at all binding sites for PPIs/2C9, which indicate that electrostatic interactions and hydrophobic interactions appear to be important for stabilizing the binding sites of most PPIs/2C9. However, in the case of Lan/2C9, the hydrophobic interactions are more important than the electrostatic interactions for stabilizing the binding site. In addition, an interesting conformational conversion from extended to U-bend structures was observed for pantoprazole, which is attributed to an H-bond interaction in the binding pocket, an internal π–π stacking interaction, and an internal electrostatic interaction of pantoprazole.

The structures and relative stabilities of CnB3 (n = 1–8) clusters are explored and analyzed at the CCSD(T)/6-311+G(d)//B3LYP/6-311+G(d) level. For low-lying isomers of CnB3 (n = 1–8), cyclic structures are more favorable in energy than branch as well as linear structures, and rings with exocyclic chains. For most isomers of CnB3 (n = 1–8), the structures with doublet states are lower in energy than the ones with quartet states. The lowest-energy isomers of CnB3 are all cyclic structures. The lowest-energy structures of CnB3 (n = 1–3) appear to be similar to those of pure boron clusters which have polycylic structures, while the lowest-energy structures of CnB3 (n = 4–8) tend to be analogous to the corresponding geometries of pure carbon, CnB, and CnB2 clusters which possess single-ring structures. The most stable structures of planar CnB3 (n = 3–8) clusters can be derived from combining a B–C–B–C–C–B building unit and a carbon chain. Some physical properties, such as the binding energy per atom, incremental binding energy, and second order energy difference suggest that for CnB3 clusters, odd-n clusters are more stable than even-n clusters. Results from NBO and molecular orbital analysis illustrate that the formation of the delocalized π MOs, the σ-radial and σ-tangential MOs are favorable to the stabilization of structures for lowest-energy isomers. It is interesting to find from the valence molecular orbital and NBO analyses that for the most stable isomers of CnB3 (n = 1–8), the numbers of π electrons for CnB3 (n = 1–8) is (n + 1) with an exception of C4B3 (6 π electrons), suggesting that CB3, C4B3 and C5B3 may have aromaticity, which is consistent with the results of the nucleus independent chemical shifts (NICS).

The main component of senile plaques found in AD brain is amyloid β-peptide (Aβ), and the neurotoxicity and aggregation of Aβ are associated with the formation of β-sheet structure. Experimentally, beta sheet breaker (BSB) peptide fragment Leu-Pro-Phe-Phe-Asp (LPFFD) can combine with Aβ, which can inhibit the aggregation of Aβ. In order to explore why LPFFD can inhibit the formation of β-sheet conformation of Aβ at atomic level, first, molecular docking is performed to obtain the binding sites of LPFFD on the Aβ(1–42) (LPFFD/Aβ(1–42)), which is taken as the initial conformation for MD simulations. Then, MD simulations on LPFFD/Aβ(1–42) in water are carried out. The results demonstrate that LPFFD can inhibit the conformational transition from α-helix to β-sheet structure for the C-terminus of Aβ(1–42), which may be attributed to the hydrophobicity decreasing of C-terminus residues of Aβ(1–42) and formation probability decreasing of the salt bridge Asp23-Lys28 in the presence of LPFFD.

Human serum albumin (HSA), the most abundant protein found in blood plasma, transports many drugs and ligands in the circulatory system. The drug binding ability of HSA strongly influences free drug concentrations in plasma, and is directly related to the effectiveness of clinical therapy. In current work, binding of HSA to angiotensin II receptor blockers (ARBs) are investigated using docking and molecular dynamics (MD) simulations. Docking results demonstrate that the main HSA–ARB binding site is subdomain IIIA of HSA. Simulation results reveal clearly how HSA binds with valsartan and telmisartan. Interestingly, electrostatic interactions appear to be more important than hydrophobic interactions in stabilizing binding of valsartan to HSA, and vice versa for HSA–telmisartan. The molecular distance between HSA Trp214 (donor) and the drug (acceptor) can be measured by fluorescence resonance energy transfer (FRET) in experimental studies. The average distances between Trp-214 and ARBs are estimated here based on our MD simulations, which could be valuable to future FRET studies. This work will be useful in the design of new ARB drugs with desired HSA binding affinity.

The geometrical structures, potential energy surface, stability, and bonding character of low-energy isomers of planar C3B3 were systematically explored and investigated at the B3LYP/6-311+G(d)// CCSD(T)/6-311+G(d) level for the first time. A large number of planar structures for low-energy isomers of C3B3 are located and reported. In particular, isomers 1 (Cs,2A’) and 2 (Cs,2A’), with a belt-like structure corresponding to the lowest-energy structures of planar C3B3, are revealed. Based on molecular orbital (MO) and natural bond orbital (NBO) analyses, delocalized σ MOs, multi-centered σ MOs, and delocalized π MOs play an important role in stabilizing the structures of low-energy isomers of C3B3. It is interesting to note from isomerization analysis that the interconversion of isomers 2 and 7 can be realized through two isomerization channels. The results demonstrate that isomers 1, 2, 3, 4, 7, 9, 12, 17, 19, and 20 of C3B3 are stable both thermodynamically and kinetically at the B3LYP/ 6-311+G(d)//CCSD(T)/ 6-311+G(d) level, and that they are observable in the laboratory, which is helpful for future experimental studies of C3B3.

The structure, phase transition, and nucleation of Au nanoparticles confined within armchair single-walled carbon nanotubes ((n,n)-SWNTs) are investigated using molecular dynamics (MD) simulation technique. The Au−Au interactions are described by the TB-SMA potentials and the Au-SWNT interactions are represented by Lennard-Jones potential. SWNTs are approximately considered to be rigid. The total energies, structures, Lindemman indices, and radial density distributions are used to reveal the feature of phase transition for Au nanoparticles confined in (n,n)-SWNTs. The classical nucleation theory is applied to perform nucleation analysis. Results demonstrate that confined AuN exhibit multishell structures. The order−disorder transformation of atoms in each layer is an important structure feature of phase transition. Interestingly, the melting starts from the innermost layer and freezing starts from outermost layer for confined Au nanoparticles. SWNTs have a significant effect on the structures and stabilities of the confined Au nanoparticles. On the other hand, some important thermodynamic and dynamic parameters are estimated and compared with available experimental and calculated results. This work provides the primary physical insights into the phase transition and nucleation process of confined Au nanoparticles.

Amyloid β-peptide (Aβ) is the major component of plaques found in the brains of Alzheimer’s patients. Among its two predominate forms − Aβ(1–40) and Aβ(1–42), the latter possesses stronger aggregation and deposition propensity than the former. To explore the conformational preference of Aβ(1–42) in different solvents, molecular dynamics (MD) simulations are performed to investigate its secondary structures in the following four solvents: hexafluoroisopropanol (HFIP), 2,2,2-trifluoroethanol (TFE), water, and dimethyl sulfoxide (DMSO). Structural analyses demonstrate that there are two stable helix regions of Aβ(1–42) in HFIP and TFE, supporting the idea that they act as helix-promoting solvents. In aqueous solution, α-helix to β-sheet conformational transition is observed in the C-terminal domain of Aβ(1–42). However, in pure DMSO, the unfolding of C-terminal region occurs, but no β-sheet structure is observed. The primary mechanism of conformational behaviors of Aβ(1–42) in the four solvents mentioned above is analyzed and discussed based on the results of MD simulations.

Aβ(1–40) and Aβ(1–42) are the two predominant forms of amyloid β-peptide (Aβ) in the plaques found in the brains of Alzheimer’s patients. They possess identical amino acid sequence except that the latter has additional two residues (Ile and Ala) at the end of C-terminus, but the latter is more prone to aggregate and neurotoxic than the former. In order to explore the reason why Aβ(1–42) has more unfolded C-terminus than Aβ(1–40) in water, we employ molecular dynamics simulation technology to investigate their different conformational behaviors in water and methanol. Results reveal that the N-terminal parts of both peptides exhibit similar structural changes, but the secondary structures of their C-terminal parts are different. In water and methanol, the C-terminus of Aβ(1–42) mainly adopts β-sheet structure, while some residues in the C-terminus of Aβ(1–40) still keep initial helix structures, no β-sheet structure is observed. The primary mechanism of different conformational behaviors of Aβ(1–40) and Aβ(1–42) in the solvents is analyzed and discussed based on the results of MD simulations.

We carry out molecular dynamics (MD) simulation studies on the phase transition and nucleation of (KBr)N clusters confined within armchair single-walled carbon nanotubes ((R,R)-SWNTs) with Born–Mayer–Huggins’ potential functions for the ion–ion interactions and simple Lennard-Jones potentials for the ion–carbon interactions. A novel crystallite of KBr cluster inside (R,R)-SWNT is observed during slow cooling or quenching runs. Some important thermodynamic and dynamic parameters are estimated. The effect of (R,R)-SWNT on nucleation and phase transition of KBr clusters is analyzed and discussed.

The DFT(B3LYP)/6-311+G(d) method is used to study the geometries, growth feature, and relative stability of 106 lower-energy isomers of monocyclic CnB4 (n = 2–9). Vibrational frequency analysis is performed to ensure the optimized isomers are stable at the same level. It is interesting to find that the formation of the lowest-energy isomers of monocyclic CnB4 (n = 2–9) is through joining –Cm– (m = 0–2) and –Cn– (n = 0–5) carbon chains by two B–C–B bridges under the constraint of C2v symmetry (or D2h symmetry if m = n). The stability of global minimum isomers is discussed based on their binding energies per atom, the incremental binding energy, second order energy difference, vertical ionization energy, vertical electron affinity, and average polarizability.

We carried out the computational studies on the geometric and electronic properties of electronic states of metastable C2N4 (m-C2N4) and corresponding ions using the CASSCF and DFT(B3LYP)/CCSD(T) techniques. The optimized geometries of electronic states, vibrational frequencies, Mulliken populations, bond orders, and average polarizabilities are computed at the DFT level while the relative energies of the electronic states, ionization energy, electron affinity, binding energy of m-C2N4 are calculated at the CCSD(T) level. The anion photoelectron spectra of m-C2N4− are also predicted. It is interesting to find that the relative energies of the electronic states of m-C2N4 cluster linearly correlate with the amount of charge transfer between N and C atoms and that, however, there is no charge transfer between C and N atoms upon electron ionization or electron attachment.

Ground and excited states of mixed gallium stannide tetramers (Ga3Sn, Ga3Sn+, Ga3Sn−, GaSn3, GaSn3+, and GaSn3−) are investigated employing the complete active space self-consistent-field (CASSCF), density function theory (DFT), and the coupled-cluster single and double substitution (including triple excitations) (CCSD(T)) methods. The ground states of Ga3Sn, Ga3Sn+, and Ga3Sn− are found to be the 2A1, 3B1, and 1A1 states in C2v symmetry with a planar quadrilateral geometry, respectively. The ground states of GaSn3 and GaSn3− is predicted to be the 2A1 and 1A1 states in C2v point group with a planar quadrilateral structure, respectively, while the ground state of GaSn3+ is the 1A1 state with ideal triangular pyramid C3v geometry. Equilibrium geometries, vibrational frequencies, binding energies, electron affinities, ionization energies, and other properties of Ga3Sn and GaSn3 are computed and discussed. The anion photoelectron spectra of Ga3Sn− and GaSn3− are also predicted. It is interesting to find that the amount of charge transfer between Ga and Sn2 atoms in the 1A1 state of GaSn3+ greatly increases upon electron ionization from the 2A1 state of GaSn3, which may be caused by large geometry change. On the other hand, the results of the low-lying states of Ga3Sn and GaSn3 are compared with those of Ga3Si and GaSi3.

We perform molecular dynamics simulations to study the homogeneous nucleation in the freezing of molten potassium bromide clusters. The nucleation rates tend to decrease with increasing cluster size and temperature. The solid–liquid interfacial free energy σsl of 42.4–52.3 mJ/m2 is close to the values predicted by Turnbull's relation and comparable to the experimental observation by Buckle and Ubbelohde. It is interesting to find that there is no cluster size effect on the critical nucleus size. Critical nucleus sizes inferred from classical nucleation theory are of 6.5–20.7 K+Br− ionic pairs in the temperature range of 400–600 K. The critical nucleus size at bulk MD freezing temperature obtained by extrapolation is about 45 K+Br− ionic pairs, which is comparable to the experimental value of NaCl.