Developing correlation-consistent numeric atom-centered orbital basis sets for krypton: Applications in RPA-based correlated calculations.

Localized atomic orbitals are the preferred basis set choice for large-scale explicit correlated calculations, and high-quality hierarchical correlation-consistent basis sets are a prerequisite for correlated methods to deliver numerically reliable results. At present, numeric atom-centered orbital (NAO) basis sets with valence correlation consistency (VCC), designated as NAO-VCC-nZ, are only available for light elements from hydrogen (H) to argon (Ar) [Zhang et al., New J. Phys. 15, 123033 (2013)]. In this work, we extend this series by developing NAO-VCC-nZ basis sets for krypton (Kr), a prototypical element in the fourth row of the periodic table. We demonstrate that NAO-VCC-nZ basis sets facilitate the convergence of electronic total-energy calculations using the Random Phase Approximation (RPA), which can be used together with a two-point extrapolation scheme to approach the complete basis set limit. Notably, the Basis Set Superposition Error (BSSE) associated with the newly generated NAO basis sets is minimal, making them suitable for applications where BSSE correction is either cumbersome or impractical to do. After confirming the reliability of NAO basis sets for Kr, we proceed to calculate the Helmholtz free energy for Kr crystal at the theoretical level of RPA plus renormalized single excitation correction. From this, we derive the pressure-volume (P-V) diagram, which shows excellent agreement with the latest experimental data. Our work demonstrates the capability of correlation-consistent NAO basis sets for heavy elements, paving the way toward numerically reliable correlated calculations for bulk materials.

Tunable Interband Transitions in Twisted h-BN/Graphene Heterostructures.

In twisted h-BN/graphene heterostructures, the complex electronic properties of the fast-traveling electron gas in graphene are usually considered to be fully revealed. However, the randomly twisted heterostructures may also have unexpected transition behaviors, which may influence the device performance. Here, we study the twist-angle-dependent coupling effects of h-BN/graphene heterostructures using monochromatic electron energy loss spectroscopy. We find that the moiré potentials alter the band structure of graphene, resulting in a redshift of the intralayer transition at the M point, which becomes more pronounced up to 0.22 eV with increasing twist angle. Furthermore, the twisting of the Brillouin zone of h-BN relative to the graphene M point leads to tunable vertical transition energies in the range of 5.1-5.6 eV. Our findings indicate that twist-coupling effects of van der Waals heterostructures should be carefully considered in device fabrications, and the continuously tunable interband transitions through the twist angle can serve as a new degree of freedom to design optoelectrical devices.

Implementation of the meta-GGA exchange-correlation functional in numerical atomic orbital basis: With systematic testing on SCAN, rSCAN, and r2SCAN functionals.

Kohn-Sham density functional theory (DFT) is nowadays widely used for electronic structure theory simulations, and the accuracy and efficiency of DFT rely on approximations of the exchange-correlation functional. By including the kinetic energy density τ, the meta-generalized-gradient approximation (meta-GGA) family of functionals achieves better accuracy and flexibility while retaining the efficiency of semi-local functionals. For example, the strongly constrained and appropriately normed (SCAN) meta-GGA functional has been proven to yield accurate results for solid and molecular systems. We implement meta-GGA functionals with both numerical atomic orbitals and plane wave bases in the ABACUS package. Apart from the exchange-correlation potential, we also discuss the evaluation of force and stress. To validate our implementation, we perform finite-difference tests and convergence tests with the SCAN, rSCAN, and r2SCAN meta-GGA functionals. We further test water hexamers, weakly interacting molecules from the S22 dataset, as well as 13 semiconductors using the three functionals. The results show satisfactory agreement with previous calculations and available experimental values.

Preferential decomposition of the major anion in a dual-salt electrolyte facilitates the formation of organic-inorganic composite solid electrolyte interphase.

The performance of a lithium metal battery (LMB) with liquid electrolytes depends on the realization of a stable solid electrolyte interphase (SEI) on the Li anode surface. According to a recent experiment, a high-concentrated (HC) dual-salt electrolyte is effective in modulating the SEI formation and improving the battery performance. However, the underlying reaction mechanism between this HC dual-salt electrolyte and the lithium metal anode surface remains unknown. To understand the SEI formation mechanism, we first performed 95 ps ab initio Molecular Dynamics (AIMD) simulation and then extend this AIMD simulation to another 1 ns by using Hybrid ab Initio and Reactive Molecular Dynamics (HAIR) to investigate the deep reactions of such dual-salt electrolytes consists of lithium difluorophosphate and lithium bis(trifluoromethanesulfonyl)imide in dimethoxyethane (DME) solvent at lithium metal anode surface. We observed the detailed reductive decomposition processes of DFP- and TFSI-, which include the formation pathway of CF3 fragments, LiF, and LixPOFy, the three main SEI components observed experimentally. Furthermore, after extending the simulation to 1.1 ns via the HAIR scheme, the decomposition reactions of DME solvent molecules were also observed, producing LiOCH3, C2H4, and precursors of organic oligomers. These microscopic insights provide important guidance in designing the advanced dual-salt electrolytes for developing high-performance LMB.

Reproducibility of Hybrid Density Functional Calculations for Equation-of-State Properties and Band Gaps.

Hybrid density functional (HDF) approximations usually deliver higher accuracy than local and semilocal approximations to the exchange-correlation functional, but this comes with drastically increased computational cost. Practical implementations of HDFs inevitably involve numerical approximations─even more so than their local and semilocal counterparts due to the additional numerical complexity arising from treating the exact-exchange component. This raises the question regarding the reproducibility of the HDF results yielded by different implementations. In this work, we benchmark the numerical precision of four independent implementations of the popular Heyd-Scuseria-Ernzerhof (HSE) range-separated HDF on describing key materials' properties, including both properties derived from equations of state (EOS) and band gaps of 20 crystalline solids. We find that the energy band gaps obtained by the four codes agree with each other rather satisfactorily. However, for lattice constants and bulk moduli, the deviations between the results computed by different codes are of the same order of magnitude as the deviations between the computational and experimental results. On the one hand, this means that the HSE functional is rather accurate for describing the cohesive properties of simple insulating solids. On the other hand, this also suggests that the numerical precision achieved with current major HSE implementations is not sufficiently high to unambiguously assess the physical accuracy of HDFs. It is found that the pseudopotential treatment of the core electrons is a major factor that contributes to this uncertainty.

Vertex effects in describing the ionization energies of the first-row transition-metal monoxide molecules.

The GW approximation is considered to be the simplest approximation within Hedin's formulation of many-body perturbation theory. It is expected that some of the deficiencies of the GW approximation can be overcome by adding the so-called vertex corrections. In this work, the recently implemented G0W0Γ0 (1) scheme, which incorporates the vertex effects by adding the full second-order self-energy correction to the GW self-energy, is applied to a set of first-row transition-metal monoxide (TMO) anions. Benchmark calculations show that results obtained by G0W0Γ0 (1) on top of the B3LYP hybrid functional starting point (SP) are in good agreement with experiment data, giving a mean absolute error of 0.13 eV for a testset comprising the ionization energies (IEs) of 27 outer valence molecular orbitals (MOs) from nine TMO anions. A systematic SP-dependence investigation by varying the ratio of the exact exchange (EXX) component in the PBE0-type SP reveals that, for G0W0Γ0 (1), the best accuracy is achieved with 20% EXX. Further error analysis in terms of the orbital symmetry characteristics (i.e., σ, π, or δ) in the testset indicates the best amount of EXX in the SP for G0W0Γ0 (1) calculations is independent of MO types, and this is in contrast with the situation in G0W0 calculations, where the best EXX ratio varies for different classes of MOs. Despite its success in describing the absolute IE values, we, however, found that G0W0Γ0 (1) faces difficulties in describing the energy separations between certain states of interest, worsening the already underestimated G0W0 predictions.

DFT+U within the framework of linear combination of numerical atomic orbitals.

We present a formulation and implementation of the density functional theory (DFT)+U method within the framework of linear combination of numerical atomic orbitals (NAO). Our implementation not only enables single-point total energy and electronic-structure calculations but also provides access to atomic forces and cell stresses, hence allowing for full structure relaxations of periodic systems. Furthermore, our implementation allows one to deal with non-collinear spin texture, with the spin-orbit coupling (SOC) effect treated self-consistently. The key aspect behind our implementation is a suitable definition of the correlated subspace when multiple atomic orbitals with the same angular momentum are used, and this is addressed via the "Mulliken charge projector" constructed in terms of the first (most localized) atomic orbital within the d/f angular momentum channel. The important Hubbard U and Hund J parameters can be estimated from a screened Coulomb potential of the Yukawa type, with the screening parameter either chosen semi-empirically or determined from the Thomas-Fermi screening model. Benchmark calculations are performed for four late transition metal monoxide bulk systems, i.e., MnO, FeO, CoO, and NiO, and for the 5d-electron compounds IrO2. For the former type of systems, we check the performance of our DFT+U implementation for calculating bandgaps, magnetic moments, electronic band structures, as well as forces and stresses; for the latter, the efficacy of our DFT+U+SOC implementation is assessed. Systematic comparisons with available experimental results, especially with the results from other implementation schemes, are carried out, which demonstrate the validity of our NAO-based DFT+U formalism and implementation.

Dysregulation of Protein Kinase C in Adult Depression and Suicide: Evidence From Postmortem Brain Studies.

BACKGROUND: Several lines of evidence suggest the abnormalities of protein kinase C (PKC) signaling system in mood disorders and suicide based primarily on the studies of PKC and its isozymes in the platelets and postmortem brain of depressed and suicidal subjects. In this study, we examined the role of PKC isozymes in depression and suicide. METHODS: We determined the protein and mRNA expression of various PKC isozymes in the prefrontal cortical region (Brodmann area 9) in 24 normal control subjects, 24 depressed suicide (DS) subjects, and 12 depressed nonsuicide (DNS) subjects. The levels of mRNA in the prefrontal cortex were determined by quantitative real-time reverse transcription PCR, and the protein expression was determined by western blotting. RESULTS: We observed a significant decrease in mRNA expression of PKCα, PKCßI, PKCδ, and PKCε and decreased protein expression in either the membrane or the cytosol fraction of PKC isozymes PKCα, PKCßI, PKCßII, and PKCδ in DS and DNS subjects compared with normal control subjects. CONCLUSIONS: The current study provides detailed evidence of specific dysregulation of certain PKC isozymes in the postmortem brain of DS and DNS subjects and further supports earlier evidence for the role of PKC in the platelets and brain of the adult and teenage depressed and suicidal population. This comprehensive study may lead to further knowledge of the involvement of PKC in the pathophysiology of depression and suicide.

Innate immunity receptors in depression and suicide: upregulated NOD-like receptors containing pyrin (NLRPs) and hyperactive inflammasomes in the postmortem brains of people who were depressed and died by suicide.

BACKGROUND: Abnormalities of inflammation have been implicated in the pathophysiology of depression and suicide, based on observations of increased levels of proinflammatory cytokines in the serum of people who were depressed and died by suicide. More recently, abnormalities in cytokines and innate immunity receptors such as toll-like receptors have also been observed in the postmortem brains of people who were depressed and died by suicide. In addition to toll-like receptors, another subfamily of innate immunity receptors known as NOD-like receptors containing pyrin (NLRPs) are the most widely present NOD-like receptors in the central nervous system. NLRPs also form inflammasomes that play an important role in brain function. We studied the role of NLRPs in depression and suicide. METHODS: We determined the protein and mRNA expression of NLRP1, NLRP3 and NLRP6 and the components of their inflammasomes (i.e., adaptor molecule apoptosis-associated speck-like protein [ASC], caspase1, caspase3, interleukin [IL]-1ß and IL-18) postmortem in the prefrontal cortex of people who were depressed and died by suicide, and in healthy controls. We determined mRNA levels using quantitative polymerase chain reaction, and we determined protein expression using Western blot immunolabelling. RESULTS: We found that the protein and mRNA expression levels of NLRP1, NLRP3, NLRP6, caspase3 and ASC were significantly increased in people who were depressed and died by suicide compared to healthy controls. LIMITATIONS: Some people who were depressed and died by suicide were taking antidepressant medication at the time of their death. CONCLUSION: Similar to toll-like receptors, NLRP and its inflammasomes were upregulated in people who were depressed and died by suicide compared to healthy controls. Innate immunity receptors in general - and NLRPs and inflammasomes in particular - may play an important role in the pathophysiology of depression and suicide.

Beryllium and Magnesium Metal Clusters: New Globally Stable Structures and G0W0 Calculations.

We study the structural and electronic properties of beryllium (Be) and magnesium (Mg) clusters for sizes 2-20 using a two-step approach. In the first step, a global search of the stable and low-lying metastable isomer structures is carried out on the basis of first-principles potential energy surfaces at the level of the generalized gradient approximation (GGA) of density functional theory (DFT). In the second step, vertical ionization potentials (VIPs) and energy gaps between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are determined using the G0W0 methods for up to the fourth-lowest-energy isomers. Novel globally lowest-energy isomer structures are identified for Be14, Mg14, and Mg16 clusters. The van der Waals interactions are found to have a stronger influence on Mg clusters than on Be clusters. A second-difference analysis for both the binding energies and HOMO-LUMO gaps reveals a close relationship between the structural stability and chemical hardness for both types of clusters.

First-principles study of benzo[a]pyrene-7,8-dione and DNA adducts.

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in environments, and some of them are causative agents of human cancer. Previous studies concluded that benzo[a]pyrene-7,8-dione (BPQ), which is one kind of carcinogenic PAH metabolites, forms covalently bonded adducts with DNA, and the major adduct formed is a deoxyguanosine adduct. In this work, we investigate the interactions between BPQ and DNA molecules via first-principles calculations. We identify six possible DNA adducts with BPQ. In addition to the four adducts forming covalent bonds, there are two adducts bound purely by van der Waals (vdW) interactions. Remarkably, the two vdW-bound adducts have comparable, if not larger, binding energies as the covalent adducts. The results may help us gain more understanding of the interactions between PAH metabolites and DNA.

All-electron ab initio Bethe-Salpeter equation approach to neutral excitations in molecules with numeric atom-centered orbitals.

The Bethe-Salpeter equation (BSE) based on GW quasiparticle levels is a successful approach for calculating the optical gaps and spectra of solids and also for predicting the neutral excitations of small molecules. We here present an all-electron implementation of the GW+BSE formalism for molecules, using numeric atom-centered orbital (NAO) basis sets. We present benchmarks for low-lying excitation energies for a set of small organic molecules, denoted in the literature as "Thiel's set." Literature reference data based on Gaussian-type orbitals are reproduced to about one millielectron-volt precision for the molecular benchmark set, when using the same GW quasiparticle energies and basis sets as the input to the BSE calculations. For valence correlation consistent NAO basis sets, as well as for standard NAO basis sets for ground state density-functional theory with extended augmentation functions, we demonstrate excellent convergence of the predicted low-lying excitations to the complete basis set limit. A simple and affordable augmented NAO basis set denoted "tier2+aug2" is recommended as a particularly efficient formulation for production calculations. We finally demonstrate that the same convergence properties also apply to linear-response time-dependent density functional theory within the NAO formalism.

Innate immunity in the postmortem brain of depressed and suicide subjects: Role of Toll-like receptors.

Abnormalities of Toll-like receptors (TLRs) have been implicated in the pathophysiology of depression and suicide. Interactions of TLRs with pathogen-associated molecular patterns (PAMP) and damage-associated molecular patterns (DAMP) initiate signaling through myeloid differentiation primary response-88 (MyD88) and produce cytokines through the activation of the transcription factor nuclear factor kappa beta (NF-kB). We have earlier shown an increase in the protein and mRNA expression of TLR3 and TLR4 in the prefrontal cortex (PFC) of depressed suicide (DS) subjects compared with normal control (NC) subjects. To examine if other TLRs are altered in postmortem brain, we have now determined the protein and mRNA expression of other TLRs (TLR1, TLR2, TLR5, TLR6, TLR7, TLR8, TLR9 and TLR10) in the PFC of DS, depressed non-suicide (DNS), non-depressed suicide (NDS) and NC subjects. We determined the protein expression by Western blot and mRNA expression levels by real-time PCR (qPCR) in the PFC of 24 NC, 24 DS, 12 DNS and 11 NDS subjects. Combined with our previous study of TLR3 and TLR4, we found that the protein expression of TLR2, TLR3, TLR4, TLR6 and TLR10, and mRNA expression of TLR2 and TLR3 was significantly increased in the DS group compared with NC group. This study demonstrated that certain specific TLRs are altered in DS subjects, and hence those TLRs may be appropriate targets for the development of therapeutic agents for the treatment of suicidal behavior.

A DFT study of energetic and structural properties of a full turn of A-form DNA under relaxed and stretching conditions.

We carried out a first-principles quantum-mechanical study of a set of full-turn A-form DNA oligonucleotides using density functional approximations. The structural features of the fully relaxed model DNA molecules and more importantly, the energetic and structural changes of these molecules under stretching conditions are examined in detail. Special attention is paid to the dependence of the structural properties on the stacking sequences of the constituent DNA base pairs. It appears that DNA oligonucleotides are extremely flexible, and structural properties such as the diameter and the widths of the minor and major grooves change regularly as a function of the stretching rate (stretching length in percentage). Additionally, we found that the length of the hydrogen bonds in the DNA base pairs varies with the DNA stacking sequence. This work indicates that rich information and insights can be gained from first principles studies of model DNA molecules of only O(102-103) atoms.

Abnormal protein and mRNA expression of inflammatory cytokines in the prefrontal cortex of depressed individuals who died by suicide

Background: Depression and stress are major risk factors for suicidal behaviour, and some studies show abnormalities of proinflammatory cytokines in the serum and cerebrospinal fluid (CSF) of depressed and suicidal patients. However, it is not clear if similar abnormalities of cytokines are present in the brain of suicidal and depressed patients. Methods: We therefore determined the mRNA (using realtime polymerase chain reaction) and protein (using enzyme-linked immunosorbent assay and Western Blot) expression levels of interleukin (IL)-1ß, IL-6, tumour necrosis factor (TNF)-α, lymphotoxin A, lymphotoxin B, IL-8, IL-10 and IL-13 in the prefrontal cortex (PFC) obtained from 24 depressed individuals who died by suicide and 24 nonpsychiatric controls. Results: We observed that the mRNA and protein levels of IL-1ß, IL-6, TNF-α, and lymphotoxin A were significantly increased, and levels of anti-inflammatory cytokine IL-10, and of IL-1 receptor antagonist (IL-1RA) were significantly decreased in the PFC of depressed individuals who died by suicide compared with controls. There were no significant differences in the protein and mRNA levels of IL-8 and IL-13 in the PFC. Limitations: The main limitation of this study is that some of the suicide group had been taking antidepressant medication at the time of death. Conclusion: Our results suggest that alterations of cytokines may be associated with the pathophysiology of depressed suicide and there may be an imbalance between pro- and anti-inflammatory cytokines in people who die by suicide. The causes of these increases in the brain of people who die by suicide, therefore, need to be investigated further.

Associations between pro-inflammatory cytokines, learning, and memory in late-life depression and healthy aging.

OBJECTIVES: Pro-inflammatory cytokines may play a role in learning and memory difficulties and may be exacerbated in late-life depression (LLD), where pro-inflammatory markers are already elevated because of aging and age-related vascular risk. METHODS: Learning and memory, and pro-inflammatory cytokines-Interleukin-1ß (IL-1ß), tumor necrosis factor-α (TNF-α), and Interleukin-6 (IL-6) were measured in 24 individuals with LLD and 34 healthy older adults (HOA). Hippocampal volumes were segmented using Freesurfer software. RESULTS: Pro-inflammatory cytokines were higher in LLD compared with HOA. Regression analyses demonstrated that educational level and right hippocampal volume significantly contributed to explaining the variance in learning. For memory performance, educational level, right hippocampal volume and a group-by-IL-6 interaction significantly contributed to the model. CONCLUSIONS: High levels of IL-6 impact cognition in LLD but not HOA. Results suggest that high levels of inflammation alone are not sufficient to account for cognitive difficulties, but may interact with other factors in at-risk populations like LLD, to contribute to memory difficulties. Copyright © 2017 John Wiley & Sons, Ltd.

Zanthoxylum alatum abrogates lipopolysaccharide-induced depression-like behaviours in mice by modulating neuroinflammation and monoamine neurotransmitters in the hippocampus.

CONTEXT: Depression is an inflammatory, commonly occurring and lethal psychiatric disorder having high lifetime prevalence. Zanthoxylum alatum Roxb. (Rutaceae), commonly called Timur, has high medicinal value and is used ethnomedicinally for the treatment of various diseases. OBJECTIVE: To evaluate the effect of hexane extract of Z. alatum seeds (ZAHE) on lipopolysaccharide (LPS)-induced depression-like behaviour in Swiss albino mice. MATERIALS AND METHODS: Mice were treated with ZAHE (100 and 200 mg/kg, p.o.) and imipramine (10 mg/kg injected i.p.) for 14 days. On 14th day of the treatment, depression-like behaviour was induced by LPS (0.83 mg/kg injected i.p.) and after 24 h of LPS administration, it was assessed by measuring behavioural parameters and biochemical estimations. RESULTS: Behavioural tests, including the open field test, forced swimming test, tail suspension test and sucrose preference test revealed that ZAHE (100 and 200 mg/kg, p.o.) and imipramine (10 mg/kg injected i.p.) alleviated the depression symptoms of LPS-induced mice. Moreover, ZAHE treatments reversed the LPS-induced alterations in the concentrations of norepinephrine and serotonin (5-HT) and inhibited the expression of brain-derived neurotrophic factor, pro-inflammatory cytokines and oxido-nitrosative stress in the mice. Acute toxicity was calculated to be LD50 > 2500 mg/kg. DISCUSSION AND CONCLUSIONS: This study showed that LPS-induced depression in mice was significantly prevented by ZAHE at both the dosages. In conclusion, ZAHE exhibited an antidepressant activity by altering monoaminergic neurotransmitters in the brain combined with its anti-inflammatory potential. Thus, it could be an effective therapeutic against inflammation-induced depression and other brain disorders.

First-principles molecular dynamics study of deuterium diffusion in liquid tin.

Understanding the retention of hydrogen isotopes in liquid metals, such as lithium and tin, is of great importance in designing a liquid plasma-facing component in fusion reactors. However, experimental diffusivity data of hydrogen isotopes in liquid metals are still limited or controversial. We employ first-principles molecular dynamics simulations to predict diffusion coefficients of deuterium in liquid tin at temperatures ranging from 573 to 1673 K. Our simulations indicate faster diffusion of deuterium in liquid tin than the self-diffusivity of tin. In addition, we find that the structural and dynamic properties of tin are insensitive to the inserted deuterium at temperatures and concentrations considered. We also observe that tin and deuterium do not form stable solid compounds. These predicted results from simulations enable us to have a better understanding of the retention of hydrogen isotopes in liquid tin.

The Expression of the Suicide-Associated Gene SKA2 Is Decreased in the Prefrontal Cortex of Suicide Victims but Not of Nonsuicidal Patients.

BACKGROUND: Recent study of genome-wide DNA methylation profiling in the postmortem brain of suicidal and nonsuicidal subjects found that gene expression of spindle and kinetochore associated complex subunit 2 (SKA2) is decreased in the postmortem brain of suicide victims compared with nonsuicidal, nonpsychiatric control subjects. METHODS: To determine if decreased SKA2 is specific to suicide and independent of diagnosis, we determined gene and protein expression of SKA2 in the prefrontal cortex obtained from suicide victims (n= 52), nonsuicidal psychiatric subjects (n= 27), and normal controls (n= 24). We determined gene expression by quantitative PCR technique and protein expression by Western blot. The postmortem brain samples were obtained from the Maryland Psychiatric Research Center. RESULTS: We found that protein and gene expression of SKA2 was significantly reduced in the prefrontal cortex of suicide victims compared with normal control subjects and nonsuicidal patients. We also found that SKA2 protein and gene expression in depressed suicide victims, schizophrenic suicide victims, and suicide victims with substance abuse and/or conduct disorders was significantly decreased compared with normal control subjects and also with nonsuicidal depressed or schizophrenic subjects. CONCLUSIONS: This study shows that decreased gene and protein expression of SKA2 observed in the prefrontal cortex of suicide victims is specific to suicide, which was not observed in the brain of nonsuicidal patients. It also indicates reduced SKA2 expression in suicide is independent of psychiatric diagnosis, since it is observed in all diagnostic groups studied. Therefore, SKA2 may be a potential biomarker for suicide.

Metal adatoms generated by the co-play of melamine assembly and subsequent CO adsorption.

Molecular self-assembly films are expected to tailor the surface process by the periodic nanostructures and add-on functional groups. In this work, a molecular network of melamine with featured pores of subnanometer size is prepared on the Au(111) surface, and is found to be able to trap the gold adatoms and concomitant single vacancies generated under the impingement of CO molecules at room temperature. DFT calculations suggest that the strong CO-Au adatom interaction as well as the high adhesion of the Au adatom inside the melamine pore could well be the driving force behind such process. This study not only sheds light onto the interactions between gasses and the metal surface that is covered by molecular self-assembly films, but also provides a novel route to manipulate the monoatomic surface species which is of catalytic interest.